Prime Directive
The Prime Directive, also known as Starfleet Command General Order 1, the Non-Interference Directive, or the principle of non-interference, was the embodiment of one of Starfleet's most important ethical principles: noninterference with other cultures and civilizations. At its core was the philosophical concept that covered personnel should refrain from interfering in the natural, unassisted, development of societies, even if such interference was well-intentioned. The Prime Directive was viewed as so fundamental to Starfleet that officers swore to uphold the Prime Directive, even at the cost of their own life or the lives of their crew, though the literal application of this oath rarely if ever applied. Instead, the use and interpretation of the Prime Directive was flexible and varied considerably, depending on the discretion of the captain or commanding officer. (; ; ; ; ; ) 

A version of the Prime Directive also applied when Starfleet vessels made first contact with new species to establish formal diplomatic relations. Although introducing the concept of alien life would alter the trajectory of any civilization, the Prime Directive permitted initial contact with a species to occur if the civilization was advanced enough technologically, even if they had not yet developed warp. Sometimes, this would involve a small scouting mission with Starfleet representatives sent ahead to establish peaceful diplomatic relations with a few delegates or scientists of that planet, before formally revealing the existence of The Federation to the planet's greater society. In those circumstances, the Prime Directive required Starfleet members to take delicate care not to disrupt local culture or customs as they decided whether to join the galactic community. However, diplomatic gift exchanges were common and permitted within limits. ()

The Vulcans used a series of protocols similar to the Prime Directive as early as 1957; in 2151, Sub-Commander T'Pol suggested to Captain Jonathan Archer that it would be wise for Starfleet to adopt these "Vulcan protocols". Later in the same year, an ethical dilemma was faced by Captain Archer and Phlox when the  encountered two species, one with a terminal genetic illness and the other without. In a foreshadowing of the Prime Directive, Archer commented that eventually, Starfleet would have to "come up with some sort of a doctrine" establishing what Humans should and should not do while exploring space and interacting with other lifeforms. In the end, they decided that interfering with the natural evolutionary course of these two species would go against the "directive" upon which they based their entire mission: to meet new species and attempt peaceful communications, not to "play God". ()

The fundamental principles were an important part of Earth Starfleet procedures as early as 2152, but it did not go into effect as a General Order until sometime after 2168. It wouldn't officially classified as the Prime Directive until around 2259 (; ; ) 

The directive remained in effect well into the 24th century and applied to at least Starfleet and Merchant Marine personnel, but specifically did not apply to ordinary Federation citizens. (; ) Despite this, it was occasionally described as a principle of the Federation or its people. (; ; )

In the 32nd century, following The Burn in 3069, the Emerald Chain flaunted the Prime Directive when it made reckless first contact with species. ()

Prohibitions

A complicated order, the Prime Directive had 47 sub-orders by the latter part of the 24th century. () However, a high-level summary was "no identification of self or mission; no interference with the social development of said planet; no references to space, other worlds, or advanced civilizations." () The directive provided guidance on what constituted prohibited "interference" with a society, covering such matters as:
 Providing knowledge of other inhabited worlds (even if individuals or governments in the society were already aware of such) to peoples who had not started using warp technology (; )
 Providing knowledge of technologies or science (; )
 Taking actions to generally affect a society's overall development (; )
 Taking actions which supported one faction within a society over another (; )
 Helping a society escape the negative consequences of its own actions ()
 Helping a society escape a natural disaster known to the society, even if inaction would result in a society's extinction, unless the society had warp technology and had formally requested aid (; )
 Subverting or avoiding the application of a society's laws (; )
 Interfering in the internal affairs of a society (; ; ; )

Scope and interpretation

The Prime Directive did not apply equally to all societies on all planets at all times. Although a cornerstone of Federation philosophy, the scope of the Prime Directive varied depending on many factors. For example, the Prime Directive primarily applied to societies that had little to no actual knowledge of other worlds and space-faring civilizations (as with certain pre-warp civilizations). (; ) But it also applied to the internal affairs of societies which knew extensively of other worlds (for example, interference in purely internal affairs by Starfleet was not permitted in the Klingon Civil War). Most Human colonies were excluded from its coverage altogether; but Human settlements established by aliens prior to official Human first contact were still covered, as they were regarded as pre-warp civilizations. (; ; ) By virtue of joining the United Federation of Planets member planets were subject to its laws, regulations, and authority. () The result was a spectrum of application: the more closely a civilization was tied to the Federation or Earth the greater the amount of interference in that civilization that was tolerated within the Prime Directive.

Some actions were clearly forbidden by the Prime Directive when it did apply to a society. Others were subject to interpretation, with commanding officers in Starfleet being given great discretionary powers regarding how and whether the Prime Directive would apply to specific situations. This promoted debate among command crews about whether the Prime Directive would (or should) apply, and how best to balance competing ethical priorities. (; ; ; ) If a decision was made by the commanding officer that could potentially be a violation of the Prime Directive, the conclusions and rationale would need to be recorded and justified to Starfleet through the ship's or station's logs. () On very rare occasions, captains could declare that the Prime Directive could be temporarily suspended for a period of time. An example of this was "The Omega Directive". () 

Any action deemed to have violated the Prime Directive (including through claiming an unjustified exception or having a weak rationale regarding actions otherwise constituting a violation) could result in punishment ranging from a formal reprimand, a possible demotion of rank, or possible arrest and court martial. However, many violations by prominent Starfleet personnel were never formally punished, and discretion was left to commanding officers on the strictness of the Prime Directive's enforcement. (; ; )

Inconsistencies and exceptions

The Prime Directive had exceptions and allowed for violations if satisfactory reasons were given. () Some examples included:

 The Prime Directive applied to "a living, growing culture"; a culture that wasn't may have been exempt ()
 Cultures already contaminated could be "repaired" but the allowed scope of those repairs is unknown (; ; )
Likewise, cultures already contaminated that could be "repaired" but the repairs do not interfere with the natural pre-contact growth of the society (; )
 A society that sent a general distress call to any space-faring culture could have been exempt (; )
 If a society already knew of and had contacted the Federation (e.g., seeking assistance; treaty matters), they could be exempted ()
 If a material injustice involving a Federation citizen would occur absent the interference, the situation could qualify. ()
 If the quadrant in which the culture resided had lost a large number of lives, an exemption could be made ()

 The society hails or attacks a Federation vessel (; )
 The society was previously interfered with by non-Federation citizens (e.g., Klingons) in a manner that would have violated the Prime Directive had it been done by Starfleet personnel (; )

 Compliance with specific orders that could not be followed if the Prime Directive fully applied (e.g., ancillary to a war with the Federation; first contact missions; diplomatic missions; trade negotiations) (; ; )
 Rescue missions ()
 The society was in diplomatic discussions with the Federation ()
 The society had been contacted by Starfleet but, upon recommendation by the contact/survey team, the planet was nonetheless subject to the Prime Directive as though such contact had not occurred (; )

There were, however, two circumstances in which the Prime Directive was suspended in its entirety. The first was when the Omega Directive applied. Due to issues of security, only Starfleet officers ranked captain and above were privy to knowledge of this directive. The existential threat to interstellar society of the dangerous Omega molecule, which destroyed subspace and rendered warp travel impossible if destabilized, outweighed the philosophical aspirations of the Prime Directive. As a result, during periods when the Omega Directive was operative the Prime Directive was fully suspended for the purpose of rendering harmless any Omega molecules and the ability to create them. () The second circumstance was General Order 24. That order permitted a starship captain, in certain circumstances, to destroy the entire surface of an inhabited planet and thereby eradicate any societies living there. ()

Federation citizens did not need an exception as the Prime Directive did not apply to them. In fact, under the rules as defined in the Directive in the 24th century, a Starfleet crew was forbidden from forcibly removing Federation citizens from a world, even if they had intentionally and materially interfered with the culture of a world in a way that would otherwise have been prohibited by the Prime Directive. ()

Attitudes toward the Prime Directive

Starfleet as an organization had the greatest respect for and required compliance with the Prime Directive. () But not all Federation citizens, or even all Starfleet personnel, believed that strict adherence to the Prime Directive under every circumstance was in the best interests of the civilizations it was designed to protect. Starfleet captains themselves had very different personal tolerances for the degree of flexibility to be applied to the Prime Directive. Captain James T. Kirk noted that the Prime Directive was intended to apply only to living, growing civilizations and felt it was appropriate to interfere where societies had been enslaved, were in a state of total stagnation (also known as an arrested culture), or even in mortal danger. (; ) Captain Kirk also at least twice attempted to interfere in the internal affairs of a civilization when he believed that higher ethics compelled or justified such actions. () On the other hand, both Captains Picard and Janeway were prepared to watch whole societies perish from natural causes rather than interfere – even when others were seeking to prevail upon them that Starfleet's role should permit actively saving societies rather than passively watching them die. (; ) This range of conduct could even be found within a single individual: Captain Janeway once opined that 23rd century Starfleet officers such as Kirk were "a little slower to invoke the Prime Directive," but she herself admitted to having "bent it on occasion" during her travels in the Delta Quadrant. ()

Shortly after coming aboard the Enterprise, Spock asked Number One if she had ever considered that the Prime Directive was not only unethical, but also illogical and perhaps morally indefensible. Chin-Riley quickly shut down this line of questioning by saying she had not, and for the sake of his sanity nor should Spock. ()

The Prime Directive as a general prohibition against interference was unique to the United Federation of Planets. Other organizations and cultures outside of Federation had different approaches to matters regarding interference with societies. These ranged from total annihilation of civilizations through assimilation (for example, the Borg), to planetary relocation when the society was endangered on its homeworld (for example, the Preservers), to providing advanced knowledge on an ad hoc basis when the society was deemed ready (for example, the Vulcans), to interfering whenever doing so was seen as vaguely amusing (for example, the Q).

However, there were societies who had similar rules against interference or sharing technology. These included the Sikarians. ()

Examples
There are many examples of actions during the 23rd and 24th centuries that were either identified at the time as violations of, or could appear to have potentially been violations of, the Prime Directive.

Interference with societies unaware of other worlds
 In 2259 of the alternate reality, Captain  learned a volcano on the planet Nibiru was going to erupt and render the Nibirans extinct. He and  went to great lengths to relocate them from their settlement before the eruption by disguising themselves, luring the natives away by stealing their sacred scroll – indirectly protecting it – and appropriating local wildlife to flee. However, Kirk chose to violate the Prime Directive anyway when he moved the  into position over the volcano to transport the stranded  before the cold fusion device he placed inside detonated, prompting the Nibirans to draw a picture of the starship in the soil and accept it as a deity. ()
 In 2259, Captain Christopher Pike  took the Enterprise to the planet Kiley 279 to investigate the disappearance of the crew of the USS Archer (NCC-627) during a First contact mission. Upon investigation, it was discovered the Kiley people had reversed-enginnered Matter-antimatter reaction into a devastating weapon due to discovering the events of the battle near Xahea the previous year by accident. To prevent the planet's inhabitants from destroying each other, Pike revealed the Enterprise to the Kiley and urged them to work for something better. The Federation Council was upset at this, but couldn't punish Pike and his crew due to the battle being classified information. They did, however, start pushing for a greater importance for General Order 1, intending on renaming it the "Prime Directive". ()
 In 2266, Captain Kirk took a landing party down to  in response to a general distress call. Once there, he and the rest of the landing party became infected with a virus that killed adults, but significantly slowed the aging process of those who had not yet entered puberty. Dr. Leonard McCoy discovered a cure for the virus, which was also given to the few children who remained alive on the planet and with whom the landing party had interacted. ()

 On stardate 3156.2, the  was trying to determine the fate of the starship . After his entire crew was threatened with death by the Landru computer, Captain Kirk caused the computer to self-destruct by convincing it that it was harming the  that it was designed to protect. Kirk justified the interference by claiming that the society was not "a living, growing culture" and that as an arrested culture the Prime Directive did not apply to it. Following the destruction of the computer Kirk left behind a team of specialists to assist the planet with societal development in the absence of Landru. ()

 On stardate 3715.3, Kirk ordered the Enterprise to destroy the Vaal computer that was caring for the inhabitants of Gamma Trianguli VI. Doing so saved his ship from destruction after the Vaal computer attacked the vessel. Kirk justified his action on the grounds that the people on the planet were essentially enslaved by a computer. As Kirk said at the time, "These people aren't living. They're existing. They don't create, produce, even think. They exist to service a machine… we owe it to them to interfere."  Despite serious misgivings from his First Officer Spock about his rationale, Kirk decided that the society was – as were the followers of Landru – an arrested culture and therefore not subject to the Prime Directive's prohibitions. ()
 On stardate 2534.0, the crew of the Enterprise investigated the loss of contact with historian and cultural observer John Gill, who had been assigned to the planet Ekos. They discovered that Gill deliberately violated the Prime Directive in an attempt to reorder the planet's society into a version of Nazi Germany. Captain Kirk acted to reduce the effects of Gill's interference in the hopes of restoring the peace that had existed before Gill's arrival. Kirk's corrective interference resulted in the overthrow of the planetary government Gill had installed and allowed for a return to such peace. ()
 In an attempt to gain diplomatic alliances and hide their activities, the Klingons surreptitiously introduced advanced (for the planet) weapons to enemies of the  on the planet Neural. Their belief was that once the Hill People were obliterated the planet would ally itself with the Klingon Empire. Discovering the interference on stardate 4211.4, Kirk felt that it was justified to "even the odds."  Through corrective interference intended to eliminate the advantages introduced by the Klingons, Kirk decided to provide the Hill People similar weapons. ()
 In 2268, Captain Ronald Tracey of the  provided material support to one faction (the Kohms) on the planet Omega IV in their ongoing war with a rival faction (the Yangs). He did so primarily through strategic advice and extensively using his phaser during at least one battle otherwise fought with bladed weapons, spears, and arrows. Tracey's rationale for violating the Prime Directive was that he believed the planet was the source of a means for Humans to significantly extend their lifetimes; he saw protection of the Kohms as the best way to allow scientific study of that means. His conclusion was that the benefits of general life extension throughout Humankind outweighed his significant interference in the planet's society. (This was echoed a century later by a similar rationale used by Admiral Dougherty in his dealings with the Ba'ku.) Tracey was subsequently arrested by Captain Kirk for his violation. (; )
 On stardate 4842.6, Captain Kirk inadvertently became entangled with the native population of the planet Amerind after his memories were damaged by an alien device. He was proclaimed a god by the indigenous population of Native Americans, married the daughter of the chief, and fathered a child with her before having his memory restored. He was later rescued by Commander Spock and Dr. McCoy, who were also inadvertently seen in full uniform by the indigenous people. ()

 Also in 2268, the USS Enterprise discovered the wreckage of the  near the planet 892-IV. A merchant service vessel, the ship and its captain, R.M. Merik had been missing for six years at that time. Upon finding the planet Merik had been convinced that carrying knowledge of the planet elsewhere would damage the highly traditional society there; he and his crew therefore beamed down to live within the society. By the time the Enterprise arrived, Merik had been elevated to First Citizen, an influential leader within the society. Captain Kirk considered Merik's interference to have violated the Prime Directive, but Merik died before he could be charged or exonerated. During this mission Kirk provided a special commendation to Montgomery Scott as "Despite enormous temptation and strong personal feelings, he obeyed the Prime Directive. His temporary blackout of the city below resulted in no interference with the society and yet saved the lives of myself and the landing party." ()

 In 2365, Lieutenant Commander Data answered a call for help from Sarjenka of Drema IV and maintained communication with her for eight weeks. Her planet was undergoing extreme seismic disturbances that the  could potentially correct. A highly emotive discussion took place among the senior staff on whether or not to interfere by resolving the problems on the planet, with mixed views on the application of the Prime Directive. The matter was settled after Captain Picard declared that the request for help allowed for an exception. Data later transported Sarjenka to the Enterprise to save her life, but her knowledge of the ship and of Data was erased from her memory. The Enterprise neutralized the seismic activity of the planet without the inhabitants being aware of it, thereby answering the call for aid while minimally interfering with the society. ()
 A malfunction in an observation team's duck blind (a holographic projection to hide a Federation cultural observation post) in 2366 caused an explosion which was viewed by the people of Mintaka III. Despite multiple attempts by the crew of the Enterprise to eliminate the societal interference (including memory wipes and secret infiltration into the society), the result of this caused the Mintakans to revert into a religious belief in an  (a god). The Mintakans had previously been on a social trajectory that included a rejection of religion, so in a final attempt to correct the inadvertent interference Captain Picard purposefully revealed aspects of the Federation to the leader of the Mintakans. This revelation showed that none of the crew were supernatural, and – while some limited knowledge of other worlds and societies remained – the corrective interference by Picard was intended to cause the Mintakans to return to their societal development as before. ()
 In 2370 Nikolai Rozhenko was acting as an assigned cultural observer for a pre-warp society on Boraal II. During and after his assignment he committed at least three actions which had Prime Directive implications. First, he intervened to save a village of people on Boraal II from the destruction of their planet from natural causes (in direct contravention of Captain Picard's orders regarding the use of his ship for such purposes). Second, he fathered a child with a native of Boraal II. Third, he elected to remain with the village following its resettlement to Vacca VI. Rozhenko's plan to save the village was to transport the entire population to a holodeck on the Enterprise. He then intended to mask their relocation and knowledge of the Federation by using holodeck technology, thereby (in his opinion) acceptably minimizing the interference in their society while they were relocated to a different planet. Captain Picard disagreed with taking any action as saving the village from a natural disaster was in his opinion a Prime Directive violation. When presented with Rozhenko's fait accompli of having already transported the village to the Enterprise as Boraal II was dying, Picard chose to resettle the village on Vacca VI while simultaneously trying to minimize the societal interference (although one native of Boraal II committed suicide after he inadvertently discovered what was happening to his people). Rozhenko was later permitted to remain on Vacca VI following the successful resettlement of the village by the Enterprise. ()

 In 2371, Captain Janeway and Lieutenant Paris both inadvertently interfered in a society on a class M planet in the Delta Quadrant and acted to repair that interference. While investigating a massive, planet-wide explosion that caused subspace to be ripped into many fractures, Janeway and Paris were transported a day back in time through one such fracture. One day later, the subsequent efforts by the crew of the starship  to rescue them caused the explosion that destroyed the surface of the planet. After the loop was completed at least once, Janeway recognized the danger presented by the rescue attempt and prevented the crew's inadvertent interference from triggering the explosion. The timeline in which the explosion never happened became the primary one such that the society was not interfered with in any respect. ()
 When two Ferengi attempted to exploit the people of  by posing as the Holy Sages of Takarian myth after they were trapped there following the disruption of the Barzan wormhole, the crew of the  decided to take them away from Takar, Captain Janeway reasoning that, even if the Ferengi were not part of the Federation, they were only present because of the Federations' actions, although she was forced to find some way to take them away from Takar without compromising the Takarians' religious beliefs and making the cultural situation on the planet even worse ().
 In 2376, USS Voyager became trapped in orbit around a planet with a unique tachyon core and subject to intense gravimetric forces, which resulted in time on the planet flowing at an accelerated rate of a day passing on the planet for every second that passed on Voyager. Due to the intense gravity forces, Voyager became trapped in the planet's orbit, where it essentially became a third pole, triggering various seismic events down on the planet, as well as serving as an inspiration of various myths and legends as it was visible as an apparent star from the surface. Although the presence of Voyager influenced the planet's culture to the point that they developed space travel just to make contact with the ship, and the issues of the Prime Directive were acknowledged when pre-spaceflight civilizations tried to make contact with the crew, it could be argued that Voyager did everything possible to leave orbit, and only had such an extreme impact on the planet's civilization due to their inability to move on and the unique temporal conditions of the encounter ().
 In 2379 the inhabitants of Kolarus III lived in isolated pockets in a pre-warp civilization at an early stage of industrial development. Captain Picard, Data, and Worf were investigating positronic signatures on the planet's surface when they were unexpectedly attacked by a group of inhabitants. An ion storm had previously prevented them using the ship's transporters, and so the away team had landed in the shuttlecraft  and were using its all-terrain vehicle to collect what turned out to be scattered portions of B4. The away team responded to the attack with suppressing phaser fire and a rapid escape. This display of weaponry, the vehicle, the crew (in uniform), and the Argo itself were all observed by the inhabitants, whose memories were left intact. ()

 In 2380, Ensign Beckett Mariner single-handedly overthrew a regime with an oppressive rat creature society eating the lizard folk. Captain Carol Freeman beamed down to immediately correct Mariner's actions. Despite Mariner proclaiming "Screw the Prime Directive!" and trying to justify saving a race, Freeman revealed that, despite it, they were quite peaceful and she had to explain why there was now an inter-species war. Fed up with everything, Freeman sent Mariner to therapy for her actions and negotiated with the now-released rat leader for food replicators. ()
 Later that same year, the  returned to Beta III, learning that the Landru computer had been reactivated. Captain Freeman and Commander Jack Ransom beamed to the surface to force the Betans back on their corrective path as it seemed that no one of the previous generation had warned them of its dangers. Freeman later complained about how someone should have kept an eye on them, but Ransom pointed out the Prime Directive forbade such an action unless Starfleet ordered them.()

Interference with societies aware of other worlds
 In 2267 Captain Kirk severely damaged a computer system on Eminiar VII. The system was used in conjunction with a Vendikar computer system to simulate war between them (rather than truly wage it). Damaging the system abrogated a treaty between the two worlds and gave the planets the choice of either waging real war or agreeing to cease hostilities. Eminiar VII, for its part, attempted to choose the latter course with the help of a Federation ambassador. The interference occurred during diplomatic discussions with the Federation, and was ancillary to Kirk's invoking General Order 24. ()

 Later in 2267, Kirk persuaded  to work for significant cultural change in the Terran Empire. Had the actions occurred in the Federation's universe they would undoubted have constituted interference in the internal affairs of other societies. However, applicability of the Prime Directive to another universe had not previously been required to be contemplated as knowledge of such universes was a closely-held secret, and apparently not known to Kirk and his crew. ()
 During a Starfleet-ordered contact to open negotiations with the Capellans for mineral resources on stardate 3156.2, Captain Kirk prevented the Teer (leader) of certain tribes from killing the wife and unborn child of the former leader. This delay resulted in her giving birth to a child who was, by lineage, to be a future leader of the tribes. The actions were a counter-response to the overthrow and death of the legitimate leader due to Klingon influence. Since the deposed leader would otherwise have remained in power absent the Klingons, actions to preserve his lineage were an attempt to "repair" the society. ()
 In 2319, then-Captain Mark Jameson of the  supplied weapons to the leader of one faction, Karnas, on Mordan IV in exchange for the release of Federation hostages. However, he also supplied Karnas' rival factions with equivalent weaponry. The net result was the affected society was plunged into decades of civil war. His rationale, later given to Captain Jean-Luc Picard, was that arming both sides was intended to maintain a balance of power, save the hostages, and negate his interference. (Jameson, however, also mentioned that he falsified records of this event to Starfleet indicating his confidence in the validity of his excuse was not as high as he later claimed.) Jameson died prior to any action being taken as a result of his interference becoming known, although Picard had previously expressed sympathy for the result of his actions, arguing that Karnas could have chosen to work for peace rather than continue his vendetta. ()
 Captain Picard interfered with the Edo society of Rubicun III on stardate 41255. First, he prevented the lawful execution of a Federation citizen (Wesley Crusher) for having inadvertently disturbed some new plantings. Second, while questioning a representative of the Edo regarding an investigation into what a powerful alien ship might do should he prevent the execution, Picard revealed that the Edo's god was an orbiting installation. Picard justified his actions to Starfleet by claiming that the execution – the sole punishment of the Edo for unlawful activity – would result in such a material injustice to Wesley that the interference in the internal affairs of the Edo was justified. ()

 When participating in a rescue mission of a J'naii ship, Commander Riker developed a relationship with Soren, who self-identified as female despite the J'naii being a genderless race and such an attitude being considered a sign of illness. When Soren's self-identification as female was discovered, she was forced to undergo psychotectic treatment to "cure" her of this; Riker appealed to Picard to rescue Soren, but Picard declined despite his sympathies for his first officer as such an action would violate the Prime Directive (Riker and Worf attempted to rescue Soren anyway, but arrived too late to prevent the treatment) ().
 In 2369, Chief Miles O'Brien took actions on the space station Deep Space 9 which interfered in the progression of a "hunt" between a group of Hunters and their quarry, a . The hunt was culturally significant to their society, and interference in the hunt was deemed by the station's commanding officer, Commander Sisko, to represent a violation of the Prime Directive. Sisko remarked that an exception permitting the interference would have existed had the Tosk affirmatively requested asylum from the Federation, but the Tosk considered such a request shameful. O'Brien's actions to nevertheless help the Tosk escape from the Hunters earned him a reprimand in his Starfleet record – although he justified his actions as restoring the hunt to its original level by allowing Tosk and the Hunters to continue as though they'd never come to DS9 – even though Sisko privately sympathized with his motives and was unofficially complicit in O'Brien's aid, ordering O'Brien to be stopped by Constable Odo … at a leisurely pace. ()
 Also in 2369, Commander Sisko offered to remove the Ennis and the Nol-Ennis from their moon prison. Dr. Julian Bashir suggested that doing so might amount to a "jail break," thereby interfering with their society's administration of justice. Sisko replied that as the commanding officer he believed the Federation would consider the artificial microbes infused into the prisoners' systems sufficient for them to be seen as "separate and unique" from their original society, while the prisoners themselves had clearly suffered more than enough for their original crime after spending so long dying and being reborn. This would make the Prime Directive inapplicable. It remained a theoretical discussion, as no one was removed from the prison due to the microbes rendering it impossible for anyone infected by them to leave the moon. ()
 In 2371 (stardate 48315.6), Captain Kathryn Janeway destroyed the Caretaker's array. This was done after the  had, as he was dying, initiated a self-destruct program. The Caretaker's reason for destroying the array was to prevent the Kazon from using it against the Ocampa – a race the Caretaker was nurturing and protecting. That program malfunctioned due to a Kazon ship colliding with the array following a battle with the Val Jean. Lt. Tuvok advised Janeway of the potential Prime Directive issues of becoming involved in internal societal matters when he said that destroying the array "would affect the balance of power in this system. The Prime Directive would seem to apply."  However, because the Kazon ship would not have collided with the array but for the unintended arrival in the system of Voyager and the Val Jean, Janeway's destruction of the array was a corrective action that reinstated the Caretaker's self-destruct plan. Her actions therefore reinstated events that would have occurred absent Voyagers forcibly becoming involved. ()
 In 2372, Lieutenant Torres assisted the Pralor Automated Personnel Units (APU) in developing a way to reproduce themselves. When first encountered by Voyager the Pralor APUs were found to be designed such that they could not create additional APUs. Torres had argued to Captain Janeway that helping the APUs to work around that design would "save them from extinction" since over time the APUs were becoming non-functional (either through age, accident, or war). Janeway refused, likening the modified design under consideration to being the "equivalent of altering their genetic structure," and therefore a Prime Directive violation. Saying that "extinction is often the natural end of evolution," Janeway refused to permit Torres to continue. The APU later kidnapped Torres and forced her, under duress, to develop a prototype that could serve as the new design standard and permit reproduction. Prior to her rescue Torres destroyed her work (in part because of revelations that the new design would be used primarily to gain advantage in a war). This action denied the APUs access to her design changes and eliminated the interference. ()
 In the early to mid 2370s, Captain Rudolph Ransom and the crew of the  killed multiple nucleogenic lifeforms and used their bodies for fuel to greatly enhance their warp drive. Ransom felt that he was justified under Starfleet Regulation 3, which provided that "in the event of imminent destruction, a captain is authorized to preserve the lives of his crew by any justifiable means." Captain Janeway rejected this reasoning, and declared his systematic murder of members of an alien society to be a direct violation of the Prime Directive. Ransom, preferring to fight both Voyager and the nucleogenic lifeforms rather than spend "thirty years in [the] brig," was eventually killed himself when the Equinox was destroyed by the aliens he had been killing. ()
 In 2373, the USS Voyager was crossing , an area of space that was completely black, inhabited only by a race that had evolved to cope without light. This area was being used by a Malon freighter to dispose of their toxic waste via a Spatial vortex that led from the edge of the Void to the heart of it. When Voyager found out what was going on, the crew initially proposed giving the Malon access to Starfleet's own recycling technology, but when this offer was rejected, they instead destroyed the spatial vortex after taking a final trip through it to the other end of the void. Although the Malon had not developed the offered recycling technology themselves, Chakotay noted that their technology showed signs of the essential framework already, with Voyager thus just offering to give the Malon a slight 'nudge' rather than offering them anything explicitly advanced, and their actions to aid the Night Aliens restoring their natural way of life, particularly since only a small portion of the Malon knew about the vortex rather than it being in mass use. ()
 In 2374, Captain Benjamin Sisko worked with Elim Garak to force the Romulan Empire to enter into Dominion War under false pretenses. The Romulans up to that point had remained neutral in the conflict. Sisko and Starfleet felt that Federation and Klingon Empire would lose the war with the Dominion if they did not gain another ally. Both Sisko and Garak, with the knowledge and approval of Starfleet Command, created false evidence that ultimately convinced the Romulans that the Dominion was planning to renege on the Peace Treaty between the two governments and mount a full scale invasion. Participation in the war by the Romulans resulted in massive military and civilian casualties within Romulan society. ()

 Captain Sisko used his superior knowledge regarding the engineering systems of the  as well as his Starfleet tactical training and experience to help the Terran Resistance Forces in the mirror universe win a major victory against the Klingon-Cardassian Alliance under the command of .

 Worf challenged and killed Gowron, Chancellor of the Klingon Empire, in 2375. Worf's motive was he believed that Gowron was deliberately mishandling Klingon forces in an attempt to destroy the reputation of General Martok, thereby risking the entire war effort against the Dominion for personal political gain. Due to this Worf had previously been authorized by Captain Sisko to use whatever means were necessary to resolve the issue. Worf defeated Gowron in single combat, and for a few moments was hailed by the assembled Klingons as Chancellor of the Klingon Empire. However, he immediately abdicated in favor of Martok, who assumed the mantle. Prior to the duel Worf removed his combadge and indicated that he was not acting as a Starfleet officer but rather simply as a Klingon. ()

 Also in 2375, Tom Paris attempted to influence the government of the Monean World Ocean to take more aggressive action to save their water-world from dissipation into space. When Paris proposed that some kind of direct interference take place to cause an otherwise recalcitrant Monean government to act, Captain Janeway declared that such interference with the internal workings of a government to be a violation of the Prime Directive. She thereafter forbade Paris from taking any such actions. Paris nonetheless attempted to destroy an oxygen refinery to demonstrate the dangers of continuing to operate them as the Moneans had been doing. His attempt was thwarted by Voyager, though. As a result Paris was demoted to the rank of ensign and incarcerated in Voyagers brig for thirty days for insubordination, unauthorized use of a spacecraft, reckless endangerment, and conduct unbecoming an officer. ()

 Finally, in 2375, Admiral Dougherty, acting on orders from the Federation Council, formed an alliance with the Son'a to forcibly relocate the entire Ba'ku population (approximately six hundred individuals) from their planet. This was intended to permit Son'a technology to collect metaphasic particles from the planet's rings and was required as the planet would become uninhabitable for decades after the life-extending particles were collected. Dougherty's rationale for interfering with the Ba'ku was that the Prime Directive simply did not apply. He stated that since the Ba'ku were not indigenous to the planet and that they "were never meant to be immortal," that removing them would simply be restoring their natural evolution. Dougherty's true motivation, however, was that collection of the particles could double lifespans throughout the Federation and that an entire new medical science would evolve as a result. Captain Picard did not accept this reason for an exception to the Prime Directive. He instead believed that Starfleet's participation in a forced relocation of a society would be "an attack on the very soul of the Federation."  Picard therefore disobeyed Dougherty's direct orders, conspired with fellow crew members to commit an armed insurrection against the admiral and his allies, and was threatened with a court martial when captured. Picard believed his refusal to accept orders that voided the Prime Directive was justified and that if "a court martial is the only way to tell the people of the Federation what happened here, then I welcome it."  Picard's actions ultimately prevented the relocation of the Ba'ku and did not result in either his loss of rank or command. ()

Other notable matters
 The Prime Directive did not go into effect as a general order until sometime after the 2160s (which is when the crew of the starship  left behind books on technology and culture that radically altered the course of civilization on the planet Sigma Iotia II). ()
 While the Prime Directive was not officially formulated until after the 2160s, the fundamental principles were an important part of Earth Starfleet procedures as early as 2152, with the crew of the  going to great lengths to recover a communicator that had accidentally fallen out of Lieutenant Malcolm Reed's pocket during a survey mission on a pre-warp planet. ()
 On stardate 43775.5, the  received a mission order from an admiral at Starfleet Command. According to the mission specifications, contact with the living spacecraft code named "Tin Man" were to include considerations for the Prime Directive. ()
 Benjamin Sisko and his crew on Deep Space 9's orders were "to do everything short of violating the Prime Directive" to make Bajor and the Bajoran people ready for Federation membership. ()

 A related order, known as the Temporal Prime Directive, was also created, mainly applicable to Starfleet officers time-traveling to the past. It prohibited them from interfering with past events, thereby altering the course of history; this included giving information about future events to individuals in the past, or taking action that would have been impossible with contemporary technology. ()
 According to Rear Admiral Norah Satie on stardate 44769.2, Jean-Luc Picard had violated the Prime Directive a total of nine times since taking command of the USS Enterprise-D three and a half years prior, with Picard countering the argument by stating that, every time he had taken action to violate the Prime Directive, it had been done with careful thought and certainty that this was the right thing for him to do, also noting that he had provided Starfleet with full reports on his reasoning for taking that action after the fact. ()

Appendices

Background information 
The  has a picture of a prop made for Admiral 's office in . This prop has text for the first three Starfleet General Orders. General Order #1's text is as follows:

As the rights of each sentient species to live in accordance with the normal cultural evolution is considered sacred, no Starfleet personnel may interfere with the normal and healthy development of alien life and culture.

Such interference includes introducing superior knowledge, strength, or technology to a world whose society is incapable of handling such advantages wisely.

Starfleet personnel may not violate the Prime Directive even to save their lives and/or their ship, unless they are acting to right an earlier violation or an accidental contamination of said culture. This directive takes precedence over any and all other considerations, and carries with it the highest moral obligation.

This phrasing of General Order One has its origins in the FASA Star Trek Role-Playing Game (The Federation sourcebook, p. 5). The text was slightly edited by the individual who made the prop for the film.

One of the TNG writers commented "who cares about Prime Directive issues?" (Cinefantastique, volume 24, issue 1, page 30)

Apocrypha 

 In the TOS novel Strangers from the Sky, Vulcans had developed their own set of non-interference canon of laws in the 1870s. However, they did not hold Humans – with whom they made first contact – bound to these restrictions. 

 In the ENT novel By the Book, Captain Archer had to decide whether to supply one of the two cultures he met with technology to bring them on the level of the more advanced society.

 In the TNG novel Double Helix: Double or Nothing the "Resolution of Non-Interference" was drafted and signed by all Federation members in 2175. By the 2190s the Prime Directive was in full force.

 In the TOS novel , a "Scale of Culture" was developed in the early 2200s in order to measure cultural development of a civilization and monitor its development.

 In the Department of Temporal Investigations novel Forgotten History, it is revealed that Kirk's last mission during the Enterprises five-year mission involved him saving a planet from an environmental crisis where the nobles were willing to allow the general population to die as a test of faith. Recognizing that this policy would result in the planet's population dying out once the crisis was over, Kirk secretly supplied the natives with the medical supplies necessary for them to survive the attack, claiming to the locals that the medicine actually came from a part of the planet that had been destroyed by earlier disasters without admitting alien interference. He was subsequently sentenced to a court-martial for violating the Prime Directive, but Kirk's argument in defense of his actions (combined with an agent of the newly-formed Department of Temporal Investigations, who wanted access to the Enterprises slingshot-capable engines) resulted in him being promoted to admiral, the court-martial board reasoning that this would be a reward to Kirk from the perspective of the public while it would privately be a punishment as Kirk wouldn't be a good fit for an admiralty position. 

 According to the CD-ROM game , one of the most serious violations of the Prime Directive was an event known as "The Galahad Incident" caused by an unauthorized entry of the USS Galahad into the civil war on Shiva Omicron IV in 2208. The Galahad used its phasers to stun an army of the Jerion faction during an attempted massacre, causing the unconscious Jerions to be themselves massacred. This eventually led to the destruction of the Jerion culture. This event became a test case for measuring the competency of a starship captain. Captain Joshua Mulrone Grant was court-martialed and imprisoned for his part in the genocide. At his court martial, he stated, "the Human Directive is the real Prime Directive."

 The Temporal Prime Directive is referenced in the novel  by Judith Reeves-Stevens. In this novel, the Temporal Prime Directive existed in both the time of TOS and in the time of TNG. There, both Kirk and Picard knew how to follow the Temporal Prime Directive, even though neither was capable of time travel (or at least not willful time travel).

 In the alternate future seen in the Deep Space Nine Millennium book trilogy, the Federation, in the middle of fighting a fierce war with the Bajoran Ascendancy, suspended the Prime Directive. The timeline was later reset thanks to the efforts of the crew of Deep Space 9.

 According to the FASA role-playing sourcebook The Federation, the first captain being court-martialed for violating the Prime Directive was Captain James Gunther Smithson. On stardate 1/2803 he disabled the nuclear weapons of two governments on Vega Proxima preventing nuclear war. Smithson was relieved of command and dishonorably discharged from service.

 In Star Trek Online, Admiral T'Nae invokes the Prime Directive in the matter between the Remans and the Tal Shiar due to the fact that there was no direct evidence that the Iconians were involved in the Remans' plight or were allied with the Tal Shiar, though gives the player clearance to pursue the matter more and take action where needed.

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