Insurrection Alpha
Insurrection Alpha was a holonovel program created by  security chief Tuvok, a realistic depiction of Voyager and its crew in which the former Maquis members rose up in armed rebellion against the Starfleet crew members.

History

Genesis
The program was originally designed in early 2371, when Tuvok believed there was a strong likelihood of a real Maquis mutiny aboard Voyager. He intended to use the holoprogram as a "tactical simulation" to train his security officers in order to prepare them for the possibility of fighting their crewmates. However, before Tuvok had completed the program, he decided that the Starfleet and Maquis crews were integrating better than anticipated, and realized that his program would only exacerbate tensions, rather than solve problems. He therefore deleted the program... or so he thought.

A few "minor" alterations
Unbeknownst to Tuvok, Seska (a Cardassian spy posing as a Bajoran member of the Maquis) discovered the program and hacked into it on stardate 48671. She created a backup version of the program with an extension that would activate the next time someone tried to change the program's narrative parameters. With this extension active, the goal of the program was to arrange for Tuvok's death, as revenge for his "betrayal" of the Maquis.

Rediscovery
The altered program lay undiscovered until late 2373, when it was found by B'Elanna Torres during a routine computer purge. She decrypted the program and played it, and quickly became fascinated by the fictional story about herself and her crewmates. She shared the program with Tom Paris, and unintentionally let knowledge of the existence of the program slip to The Doctor; soon, the whole thing became an open secret among the Voyager crew. After Paris discovered that the program came to an end just after Janeway and Paris returned to Voyager to try and retake the ship, the program became the topic of a senior staff briefing, prompting Tuvok to admit that he was the author and explain his reasons for creating the original program. Rather than get upset about the potentially inflammatory material that the holoprogram addressed, Captain Janeway endorsed a continuation of the program for entertainment purposes on the ship, citing a need for original sources of entertainment because of their long distance from the Federation.

Tuvok and Paris agreed to collaborate on writing the rest of the program, albeit with different agendas. However, when the two officers attempted to access the narrative parameters, they unintentionally triggered Seska's modifications, which not only disabled the holodeck safeties and sealed access to the holodeck controls, but also sabotaged any system on the ship which could be used to rescue them.

In Seska's altered program, members of the Voyager crew were disturbing mirrors of the real people; for example, The Doctor "treated" a phaser wound Paris had received with nitric acid, before strangling Tuvok. Booby traps (such as rigged phaser rifles and exploding EPS conduits) were planted around the ship as well, and the program itself was designed to adapt itself to any outside changes that would give those participating in it an advantage.

Ultimately, Captain Janeway was able to gain access to the program's narrative and character parameters from outside the holodeck, and altered the program sufficiently to allow Tuvok and Paris to rig a booby trap of their own, which "killed" the Seska hologram, somehow ending the program. ()

Holoprogram plotline
Note: The main storyline could change depending on how one interacted with it.
In the program, a participant assumed the identity of a Starfleet security officer with the rank of ensign. The first scene was in the corridor, where the participant spoke with Chakotay and he discussed a possible mutiny, through portraying Captain Janeway and Tuvok as unpopular. He informed the participant that there were going to be some changes aboard the ship, and that all of the Maquis and about twenty-five of the Starfleet officers were willing to support him. If the participant agreed, they were told to put the crew quarters on lock down when the time was right.

On the bridge, the participant took an aft console as they watched a conversation between Janeway and Chakotay. Janeway was leaving on an away mission with Tom Paris, leaving Chakotay in charge. When they both left the bridge, Chakotay approached the participant and asked a question confirming that the internal sensor upgrade was complete, a code phrase asking if the lock down had been successful. Two security officers subsequently arrived on the bridge and gave Chakotay a report. He then called over communications to commence the mutiny. At this point, Chakotay and the security officers attacked the bridge crew. The participant would have the chance to take out the bridge crew or the mutineers.

Follow the mutineers
If the participant followed Chakotay, they would be called to assist in a quarrel in the mess hall. Working with Seska and Chakotay, the participant helped to stop any retaliation from officers in the mess. Neelix, who originally tried to start a counter-revolution, then switched sides and joined Chakotay, ordering the others to drop their weapons. The participant then helped Seska to take the remaining officers locked in quarters to a cargo bay so Chakotay could talk to them.

In the cargo bay, Chakotay would give a speech asking people if they wished to join his side. Those who joined became part of the Maquis crew who would find a way home without stopping for any irrelevant anomalies and forgetting "almighty" Starfleet principles in favor of focusing on acquiring any necessary technology that might shorten their journey. Crew that did not comply were beamed down to the nearest class-M planet, along with the senior staff, whom Chakotay did not give an option.

On the bridge two days after the mutiny, everything would be in order, but the warp engines would be offline due to apparent sabotage. Janeway's shuttle would appear and Chakotay would try to persuade her not to intervene and would give her supplies to buy her off. She did not comply and secretly beamed on board Voyager to free the officers trapped in the brig. While doing so, Chakotay and others would find Janeway and Paris freeing the prisoners. The program would then stop abruptly, as no subsequent narrative had been programmed.

Against the mutineers
Going against the mutineers would most likely result in a stun by either Chakotay or one of the two security officers. The participant would then miss the mess hall and crew collection scene and would go straight to the cargo bay. Chakotay then gave the same speech asking Starfleet crewmen to join him, and the participant had the chance to join or stay with Starfleet. If they did not comply, they would be sent to the brig until Janeway and Paris came and tried to save them. If the participant finally agreed to join Chakotay's rebellion, he would become so suspicious of their motives that they would be assigned to lubricate the warp plasma manifolds. The program then stopped abruptly.

Alternate approaches
Neelix mentioned his own efforts to go through the program, attempting to send an encoded message to Janeway's shuttle before he was caught by Chakotay and phasered, causing the program to reset. He speculated that, on his next attempt, he would pretend to go along with the insurgency and then stage a counter-strike.

Possible continuation 
When Tom Paris assumed the writing assignment upon Tuvok opting not to, Paris suggested that Captain Janeway retake Voyager and decides to execute all the conspirators. While Tuvok protested due to the fact that Janeway would not do that in reality, Paris believed that what kept participants interested was "unexpected plot twists." He also sarcastically suggested adding a "steamy love scene between the Starfleet conn officer and the Maquis engineer," a reference to the relationship between himself and B'Elanna Torres, in response to her observation that the story had been all action so far and required something else to engage the readers. Neelix suggested an edit of previous material on the grounds that his character would never have so quickly betrayed Janeway in that manner, while The Doctor also had several suggestions for new chapters and dialogue edits.

Seska's version 
On stardate 48671, Seska discovered the program and reprogrammed it so that, when Tuvok accessed the narrative parameters file, he and anyone else with him at the time started off in the brig. There, a holographic version of Seska interacted with them, telling Tuvok that what he was experiencing was payback for his undercover infiltration of the Maquis prior to Voyager being stranded in the Delta Quadrant. She then gave them ten seconds to flee before she opened fire.

Characters were radically different to their real-life counterparts; The Doctor injected Tom Paris with nitric acid and strangled Tuvok before throwing them out when the two entered sickbay. Chakotay was also very attracted to Seska, the two sharing a kiss after they killed Captain Janeway, and was more willing to harm anyone who opposed him in contrast to the original holographic version of him, who preferred to take the ship without any bloodshed. The holographic characters were also programmed to recognize the real-life participants, as shown when Janeway called Tuvok and Paris by their names, unlike the original program made by Tuvok, in which whoever was participating was merely an unnamed ensign.

In addition to the characters behaving differently, the holodeck safeties were offline and any means of freeing those in the program were immediately sabotaged upon activation of the program; the power grid would explode if the holodeck doors were opened or if the self-destruct on the holographic Voyager was triggered, and the transporters were disabled; anyone in the program was also prevented from using the comm system to contact those outside the holodeck, though limited communication was possible by programming messages onto consoles. The program was also adaptive to any external changes made by the Voyager crew outside the holodeck, such as Seska shooting down Chakotay when he was reprogrammed to be more merciful towards their captives. Tuvok speculated that it was impossible to implement relatively major changes to the program.

Excluding the program ending in a victory for the Maquis and the deaths of all real-life participants, the program only ceased once Seska was killed; since the holographic Voyagers self-destruct or opening the holodeck doors would result in the power grid exploding, either of these actions would also terminate the program, although Seska's death was the only known way of doing so without damaging the real-life Voyager or killing any of its crew. ()

de:Rebellion Alpha
Holographic programs