Affliction (episode)
While Enterprise visits Earth for the launch of Columbia, Phlox is kidnapped and forced to help the Klingons deal with a grave threat toward their species. (Part 1 of 2)

Summary

Teaser 
A Klingon scientist works in a laboratory, watched by a Klingon general and a guard. A representation of a DNA helix is displayed behind the scientist. A door opens and a Klingon prisoner is led into the laboratory by two soldiers of the Klingon Empire. In Klingonese, the prisoner claims that his death sentence was commuted and demands to speak with the magistrate who presided over his trial. The Klingon soldiers strap him to a chair and hang a vial of green liquid above his head, which the scientist injects him with. Confused, the prisoner wails as his cranial ridges ripple and begin to dissolve.

Act One 

"Captain's starlog, November 27, 2154. We've returned home for the official launch of our sister ship, Columbia. On a personal note, I'll also be saying goodbye to one helluva chief engineer."

Returning to Earth,  finds the  starship Columbia in the orbital drydock facility, undergoing final preparations for her maiden voyage.

Meanwhile, Commander Tucker is packing a technical manual for Enterprise into a bag. He stops to look through a window in his quarters as the construction work to Columbia is being completed. When T'Pol enters his quarters, Trip remarks that the new starship is beautiful. The Vulcan states that Enterprise and Columbia are virtually identical, although Trip claims that an experienced engineer can see the differences between the two. Tucker notifies T'Pol of a "going away party" in the mess hall later and asks if she will be there. T'Pol says she doesn't understand the logic behind the engineer's departure and Trip eventually explains that he will find serving aboard Columbia more challenging. He believes he can fine tune Columbia in half the time it took him to do for Enterprise. He claims that T'Pol is not the reason for his transfer and that there are other considerations in his life, apart from her. Upon hearing this, she departs the engineer's quarters.

In San Francisco, Doctor Phlox and Ensign Hoshi Sato exit a restaurant called "Madame Chang's". Phlox is surprised that the place was so busy, although Sato explains that she told a few of her Starfleet friends about the restaurant. Phlox tells her that, earlier in the day, the organizers of the Interspecies Medical Exchange asked the doctor if he would like to serve as their Director of Xenobiology. Phlox states that he is considering the offer, although he would find it difficult to leave his shipmates on Enterprise. Suddenly, two shadowy figures step out of an alleyway and order Phlox to accompany them. When the Denobulan voices his confusion, one of the men aims a disruptor at the doctor. Sato uses her knowledge of Aikido against the men but another hooded assailant appears behind her and knocks her to the ground. Phlox is struggling with one of the men when a disruptor blast hits him, rendering him unconscious. The doctor is restrained and carried away as Hoshi lies on the ground, barely conscious. As her eyes flutter, the linguist hears one of the men say something in an alien language.

Later, when Captain Archer and Lieutenant Reed arrive at the scene of the crime, they meet Commander  of Starfleet Security. Sato tells Archer and Reed that she is fine and recounts that there were three men who came out of the shadows. Collins recalls that the ensign had told her the men spoke in a foreign, or alien, language. Collins tells Archer and Reed that the only DNA which Starfleet Security found belonged to Sato and Phlox. However, the security officers also detected some ionization traces nearby. Reed believes that the men were beamed away, although Collins explains that very few individuals have obtained transporter technology which would leave ionization traces. Collins presents the possibility that the men may have been organized by the same Human who attacked Phlox several months ago. () Reed, however, doubts that – having taken part in the brawl along with Ensign Mayweather, he feels quite confident that said drunken loudmouth would not be capable of such a well-executed plan. Collins informs Archer that Starfleet Security will continue to thoroughly investigate the crime and leaves the captain and Reed. Archer orders the lieutenant to check whether Starfleet Operations satellites picked up any transporter activity at the approximate time that Phlox was captured. Reed acknowledges and walks away.

Aboard Columbia, Tucker informs the engineering staff that they will have to align the dilithium matrix to within 0.3 microns. When Ensign Rivers replies that Tucker's order doesn't correlate with the 0.5 written in one of the tech manuals, Tucker answers that he probably has more practical experience than the warp field specialist who wrote the manual does. He orders Biggs and Pierce to recalibrate the warp field stabilizers and asks Rivers and Strong to start work on the injector assembly. As the engineers begin their duties, Tucker notices that Captain Hernandez has entered engineering. The captain reminds him that it is Starfleet protocol for a transferred officer to report to the captain when they come on board and asks Trip to come to the captain's mess for a meal later the next day. Before she leaves, Hernandez advises him to report to the quartermaster and update his uniform patch.

In the captain's ready room aboard Enterprise, T'Pol enters and informs Archer that the Denobulan ambassador has notified Phlox's wives of the doctor's kidnapping. Archer tells the Vulcan that although Sato was barely conscious, the linguist thought she heard Phlox's kidnappers say something in an alien language. Archer asks T'Pol to conduct a mind meld with Sato. When the Vulcan worries that she has never initiated a meld before, Archer replies that he will advise her with the knowledge he gained from carrying Surak's katra.

Meanwhile, in Enterprises armory, Lieutenant Reed is puzzled when he discovers that Starfleet satellite grid 137 was off-line for maintenance at the time that Phlox was kidnapped. When he contacts Starfleet Operations, there is no reply. A Human male dressed in dark clothing appears on the viewscreen which Reed was using to check the satellites. The man, , claims he will tell Reed why the satellite grid was down if the lieutenant meets him at a specific address in San Francisco.

In a darkened room, T'Pol tries to meld with Sato. When the ensign senses the meld isn't working, Archer suggests that the Vulcan try to slightly relax her emotional suppression. Eventually, their minds merge. T'Pol helps Sato remember the time just after she and Phlox had left Madame Chang's. The Vulcan appears in Sato's mind and the ensign indicates to the shadowy figures before they were assaulted. When they begin their assault, Sato struggles to focus. The ensign manages to focus long enough, however, to remember the men's words. She realizes that the aliens spoke in the Rigelian language.

On the bridge, T'Pol reports to the captain that a  left Earth approximately two hours after Phlox was captured. The freighter was scheduled to travel to Proxima colony, although the vessel's trajectory would suggest it was heading elsewhere. Canceling shore leave for the crew on Earth, the captain orders T'Pol to make sure that all officers are returned to Enterprise. He exits the bridge to contact Admiral Gardner in his ready room.

At night in a foggy San Francisco, Reed meets up with the man he spoke to earlier. The lieutenant soon discovers that Harris was involved in shutting down the satellite grid. When Reed asks him if he knows Phlox's location, Harris answers that the section he is working for requires Reed's help. The lieutenant implies that he used to be employed by the same section, although he believed his tenure to be over. Harris claims that if Reed doesn't provide the assistance which is required, Phlox may die.

Act Two 

In the same laboratory where experiments were conducted earlier, the Klingon general, K'Vagh, watches the scientist prepare another vial of green liquid to be tested. Restrained by two Klingon soldiers, Phlox is led into the lab. K'Vagh welcomes the Denobulan to the Qu'Vat Colony and warns him he will die unless he cooperates with Doctor Antaak, the Klingon scientist. When Phlox assumes he will be assisting Antaak, the general corrects him that he will be in charge. Antaak recognizes Phlox from an IME Conference on Tiburon in 2149. When Phlox fails to recall Antaak, the scientist claims he was disguised as a member of the Mazarite delegation because Klingon medics weren't invited to the meeting. As K'Vagh leaves, he states that he expects Phlox to prepare a progress report by sunrise on the following day. Antaak apologizes for the general's impolite behavior, a characteristic of the warrior caste. The scientist reveals that the Klingons are facing their greatest threat since the Hur'q attacked the Empire – an infection which has claimed millions already. Antaak fears the Klingons may become extinct if the infection isn't stopped. Phlox wonders why the Klingons didn't just ask Starfleet for help, and Antaak replies that would have made the Klingons look weak and dishonorable. The scientist recalls how Phlox's paper on viral propagation impressed him and tells the Denobulan he is interested in metagenic research. Antaak encourages Phlox to begin mapping the virus's nucleotides, and repeats that the virus is a great threat to the Klingon people – while he didn't like resorting to abduction any more than Phlox, it has occurred, and the need for his medical skill is very real.

On the bridge of Enterprise, T'Pol reports that she is no longer detecting the Rigelian freighter's warp trail. Reed suggests that the freighter could have resumed its course on impulse power and Travis Mayweather mentions that Enterprise will intercept the vessel in 8.2 hours. When Archer hails engineering, no-one responds. The captain eventually speaks to his new chief engineer Commander Kelby and tells the engineer that Enterprise needs more acceleration. Kelby says he'll try to increase the starship's velocity.

On board Columbia, Trip Tucker and Captain Hernandez are enjoying a meal. Tucker remarks that the food tastes good, and Hernandez recalls that when she left her last assignment, Republic, she stole Captain Jennings' chef. Tucker laughs, although his expression turns serious again when the captain makes him aware of two crew transfer requests since his transfer to Columbia. Not willing to reveal any names, Hernandez adds that she denied them their requested transfers, stating that engineering is already short-handed as it is. She comments on the impression Trip seems to have made with the engineering staff. Tucker doesn't care about his impression as much as he does about his staff's work. He notifies the captain that Columbia is almost ready for warp trials. Hernandez remembers that in an interview she saw with Tucker after Enterprise returned from the Xindi mission, the commander said he couldn't imagine serving on any other vessel. She wonders what changed his mind. Trip explains the crew of Enterprise were becoming too familiar and that he sometimes prefers working with colleagues rather than friends.

In T'Pol's quarters, the Vulcan is meditating. In her mind, she and Tucker are in a completely white place. She asks him why he is with her, as he isn't usually in her meditations. Tucker replies that the same question puzzles him and T'Pol explains that they are in her meditation. Tucker comments that he doesn't find the white place as interesting as a beach or the Fire Plains she showed him on . When T'Pol asks Tucker to leave her meditation, the engineer retorts that she should leave and reveals that the white space is his daydream. Rivers disturbs Tucker's reverie and the commander returns to the real world. Rivers hands him a diagnostic on a PADD and walks away.

In her quarters, T'Pol is puzzled by her meditation. Archer contacts her from the bridge and informs her that Enterprise is nearing the coordinates of the Rigelian freighter. Rising to her feet, the Vulcan tells Archer that she is heading to the bridge.

Later, the bridge's viewscreen displays the wreckage of the Rigelian craft. T'Pol determines that all of the vessel's Rigelian complement are dead and that there are no Denobulans on board. When Archer questions Reed if he can identify the vessel's destroyer, the lieutenant checks the sensors which state that the weapon signatures are have been successfully identified. However, Reed erases the alert from his screen and lies to the captain that he can't verify an identification. Believing the lieutenant's deception, Archer orders him to scan for the ship's data recorder.

On Qu'Vat Colony, Phlox believes that the Klingon virus is a mutated form of the Levodian flu. Antaak remarks that the virus is highly immune. Phlox suggests contacting the IME, who may have experience of dealing with the virus. The Denobulan adds that no-one at the IME would have to know specific details. However, Antaak sees no reason for the IME to become involved, as the Klingons stole their entire medical database. Phlox and Antaak discuss the morals of stealing medical research. Soon, General K'Vagh returns with another prisoner and a guard. Phlox examines the prisoner and concludes that the Klingon has been infected. The Denobulan worries that he and the uninfected Klingons are being exposed to the virus but Antaak reassures him that the infection only becomes contagious at stage three – the prisoner is currently only at stage one. 
When Antaak draws a weapon and aims it at the prisoner, Phlox stops him before he fires it. The Klingon scientist and Denobulan doctor argue about the ethics of euthanasia. Suddenly, K'Vagh removes a disruptor from his belt and kills the patient himself, leaving Antaak and Phlox shocked.

In his quarters, Reed opens a secure channel to Harris. The lieutenant communicates his frustration that the section of Starfleet which Harris works for destroyed the Rigelian freighter. When Reed asks what the complement of the Rigelian ship was, Harris refuses to reply. Reed discloses that he has completed an analysis of the weapons signatures and that he hasn't told Archer the identity of the destroyer vessel yet, although he doesn't know how long he'll be able to keep that information secret. Harris implies that Reed could say Orion raiders destroyed the Rigelian vessel since they operate in the area but the lieutenant suggests divulging his secret to Captain Archer. Harris reminds Reed of Archer's duty as a captain and advises the lieutenant to become comfortable with Harris' orders. He recalls that Reed agreed to serve Harris' section long before he was assigned to Enterprise. As an explosion rocks the ship, Hoshi hails the crew and orders the crew to man the battle stations. Shortly before Reed closes the channel to Harris, he explains that Enterprise is under attack.

Act Three 
As a Klingon ship fires its disruptor cannons at Enterprise, Reed falls out of a turbolift onto the bridge. T'Pol announces that the Starfleet ship's hull plating is holding, although the Klingons are not responding to Ensign Sato's hails. Archer orders Reed, now at his post, to target the warship's weapons.

Meanwhile, a Klingon boarding party transports into a corridor on Enterprise and shoots an officer who tried to call for help. Unlike usual Klingons, the members of the away team are missing their cranial ridges. They race through the corridor and enter an access tube.

On the bridge, Sato confirms the presence of the intruders. Archer instructs Reed to seal the access tube where the Klingons are and deploy a team of MACOs.

When one of the Klingon attackers races to a computer panel, another Klingon, Marab, issues the officer an instruction in Klingonese. The MACOs arrive and fire phase rifles at the Klingons. Marab shoots back but the MACOs hide from view and none are injured by the Klingon's disruptor fire. Using a communicator to contact his ship, Marab orders the warship to target the MACOs' location.

In space, Enterprise fires its phase cannons at the Klingon craft. However, the warship thrashes the Starfleet vessel, pounding the starship with its disruptor cannons as it swoops downward before it slowly recedes.

On board Enterprise, Marab watches as the section where the MACOs are located explodes, forcing them to retreat.

On the bridge, Archer authorizes Reed to disable the Klingon ship to prevent it from escaping.

Meanwhile, the Enterprise computer terminal that a member of the invading boarding party is working on displays Klingon text and graphics, which the Klingon soon disguises and returns to Starfleet characters. Satisfied that their work is completed, the Klingons head to the area of the ship where they beamed aboard. On the way there, however, Marab is shot by a MACO and lands beside a bulkhead. Another of the Klingons fires back and the MACO is thrown to Enterprises deck by his disruptor blast. The boarding party is forced to flee when they become aware of armed security officers running towards the Klingons' position. When they depart, they leave Marab behind, who the security officers find.

On the bridge, T'Pol and Travis detect that the boarding party has transported aboard the warship, which has activated its warp drive. At Archer's command, Travis attempts to pursue the Klingons but the helm station doesn't respond.

When Archer later enters sickbay and questions Marab, the captain, T'Pol and Hoshi Sato are surprised to discover that their prisoner is Klingon, as Marab is missing the cranial ridges which are a usual feature of his species.

Later, Archer, T'Pol, Sato, Mayweather and Reed gather on the bridge. Reed theorizes that Marab may have been surgically altered to appear Human. T'Pol states that because the boarding party disabled Enterprises antimatter flow regulators, the starship's warp drive should take six hours to be repaired. The captain orders Travis to help Chief Engineer Kelby in analyzing the extent of the Klingons' damage. As Reed listens, T'Pol informs Archer that the data which was stored in the Rigelian freighter's data recorder has been erased. T'Pol complies with the captain's request to work with Sato in an attempt to reconstruct the data.

On Qu'Vat Colony, Boshar – Antaak's pet targ – nibbles at Phlox's clothes. Antaak shouts at the animal to return to its domain. The Denobulan doctor is appalled when he finds Augment DNA in the mutagenic virus. General K'Vagh explains that the Klingon Empire could not allow the Human Augments, two of whom boarded and commandeered a Bird-of-Prey, to provide Starfleet with a superior advantage. Phlox argues that the Augments who were genetically engineered by Arik Soong were relics from a time from decades ago before Starfleet banned genetic engineering. K'Vagh tells Phlox that the Vulcans weren't very persuasive when they told the same story to the Klingon High Council. When Phlox remembers that all of the Augments which Soong created were killed, he wonders where the Klingons obtained the Augment DNA. Antaak replies that several embryos were found on board the Bird-of-Prey which the Klingons used to resequence the DNA of some test subjects. However, the subjects exhibited several unexpected side effects – their cranial ridges began to dissolve and they were more aggressive than the other Klingons had anticipated. For a time, it seemed that the experiments had been successful. The Klingon Augments were stronger and more intelligent, though they later suffered an excruciating death when their neural pathways began to degrade. One of the test subjects was suffering from the Levodian flu, which was modified by the Augment genes to become airborne. When Phlox becomes irritated that he wasn't given this information earlier, K'Vagh orders him to return to his work.

Aboard Enterprise in the situation room, T'Pol suggests to Sato that using a recursive algorithm may help to reconstruct the directory of the Rigelian data recorder. When Sato asks T'Pol about the side effects of a mind meld, the Vulcan replies that the procedure entails the sharing of subconscious thought. These thoughts can sometimes surface during sleep, causing strange dreams. Sato continues by admitting that she recently had a bizarre dream – one in which Trip was involved. As T'Pol listens intently, she learns that Sato's dream shared a certain parallel with the meditation she experienced earlier – Trip was in a strange, white place. 
Sato reveals that although she has never dreamed about Commander Tucker before, her dream had a romantic quality to it. T'Pol hears a console signal, returning her attention to the computer's analysis of the data recorder.

Later, Archer, T'Pol and Sato are in the captain's ready room. Archer holds a microdyne coupler which was used to erase the data recorder's memory core. The coupler was found in storage locker C-14, which was last accessed by Malcolm Reed.

Archer later calls Reed to the captain's ready room. There, the lieutenant hears the evidence against him. Reed acts as if he is innocent and insists that the Rigelian freighter was attacked with Orion weapons. Archer contends that T'Pol examined Reed's analysis and concluded that Klingon disruptors destroyed the freighter. When Archer asks for an explanation, the lieutenant refuses to answer. The captain opens the door of his ready room, where a MACO corporal, W. Woods, stands. Relieving Reed of his duties, Archer orders the MACO to escort the lieutenant to the brig and confine him there.

Act Four 
In Enterprises brig, Archer informs Reed that the starship is heading into Klingon territory, a dangerous place to go. The captain asks Reed if he knows where Phlox is, but the lieutenant assures Archer that he doesn't. Archer seems appalled and surprised that Reed would commit treason, although the armory officer insists that he isn't working for the Klingons. When the captain asks who did recruit Reed, the lieutenant doesn't answer. He implies that he has an obligation to withhold certain information and is disgraced by the thought of his father, Stuart Reed, learning that Malcolm is facing court martial.

On Qu'Vat Colony, General K'Vagh has become impatient with Phlox. The doctor notes that Arik Soong would have been able to map the virus more efficiently than the Denobulan. Antaak states that the Klingons tried to abduct Soong but he was under heavy guard. K'Vagh reveals that the Klingon High Council has launched a fleet of ships which have annihilated N'Vak Colony, one of the first planets to be infected. Phlox is appalled that the victims of the plague are being massacred, although K'Vagh argues that the Council are absolutely determined to contain the outbreak. When the Denobulan notifies K'Vagh that the development and testing of an antiviral agent will take weeks, the general worries that millions of Klingons will have been infected by that time. He tells Antaak that the fleet will reach Qu'Vat Colony in five days, although the scientist claims that the Council wouldn't order the colony's destruction if they learned that Klingon Augments had been created there. Although the experiments haven't been successful yet, Antaak informs K'Vagh that he and Phlox may be able to sustain the Augments' DNA. If successful, K'Vagh could then use the Augments to force the High Council into allowing more time for the research of a cure. When Phlox refuses to cooperate in the creation of the Augments, K'Vagh pulls a disruptor from his belt and orders a Klingon soldier to take the Denobulan away.

On Columbias bridge, Captain Hernandez contacts the dockmaster, who permits the starship to depart. She then hails Engineering, where Trip is ensuring that final preparations are complete. Ensign Rivers reports that the dilithium matrix is stable and the drive coils are properly configured. Trip notifies the captain that engineering is ready, so Hernandez gives the order to engage aft thrusters as Columbia departs spacedock, before going to warp.

In space, the new starship launches from the orbital dry dock station, before plunging into the depths of space at warp speed.

Aboard Enterprise, a partition within the brig's cell has been added, dividing it into two. Reed watches as a couple of MACOs enter and push Marab into one of the cells. As the MACOs exit, the lieutenant speaks with Marab, who thinks Reed is fortunate to be alive after lying to the captain. He reveals that if a Klingon betrayed their captain, he would be immediately executed. Reed claims that his goal is the same as Marab's – a cure. Suddenly, the starship shudders.

On the bridge, Travis reports a malfunction in the matter/antimatter intermix chamber. The pressure of the warp plasma is increasing and the anti-matter flow regulators are locked open. T'Pol is unable to determine whether the Klingons damaged the regulators. Travis states that the pressure of the warp plasma is approaching critical levels. If Enterprise dropped to impulse velocity, the warp reactor would breach. However, if the starship's speed increases, the pressure of the warp plasma would fall. Archer instructs Travis to go to maximum warp and orders T'Pol to assist the engineering crew.

In the brig, the captain demands Marab to instruct Archer how to repair the damage which the Klingons did. When the captain explains that Marab will die if Enterprises reactor breaches, the Klingon states that he is prepared to die. When Reed shouts that he can help, Archer leaves the brig, not listening to the lieutenant's pleas.

In Main Engineering, T'Pol and Kelby learn that the warp matrix has been compromised by a Klingon subroutine, which has also infiltrated the command protocols. Although T'Pol is uncertain whether she will able to remove the subroutine, she states that she will try her best to help regain control of the ship.

In a turbolift, Archer is contacted by Travis, who tells the captain the warp plasma pressure is rising again. The captain orders Travis to increase Enterprises velocity to warp 5.2, a speed which the starship won't be able to hold for long. Eventually, the ensign complies and the starship races through space to an uncertain fate.

TO BE CONTINUED...

Memorable quotes 
"It wasn't my idea to abduct you. Nevertheless, you are here. Millions of lives are at risk!"
 - Antaak, to Phlox

"I don't know who's in charge of your mess hall, but he'd give the chef on Enterprise a run for his money."
"I stole him from the Republic. Captain Jennings said I could have anything I wanted when I left, so I took his cook."
 - Captain Hernandez, to Trip Tucker, as they enjoy a meal together in her mess

"This is where I go in my mind."
"Wow! I would've thought you'd pick a more interesting place, like the beach or... one of those fire plains you showed me."
 - T'Pol and Tucker, concerning the setting for her meditation (his daydream)

"We should contact the IME – they may have seen this mutation before. I'm certain they'll be willing to share their database with us. I know of a few... indirect channels – no one would have to know."
"There's no need to contact them. We've acquired their entire database!"
 - Phlox and Antaak

"You stole it!"
"Medical research isn't a priority for the High Council – I am forced to obtain information however I can."
"That doesn't sound very honorable."
"Given the choice between honor and saving lives, I choose the latter."
 - Phlox and Antaak

"Perhaps you should ask your superiors to steal a genome sequencer, hmm? We're not going to be able to map the virus without the proper technology."
 - Phlox, to Antaak

"When I asked you to bring me a subject for dissection, I assumed he would already be dead."
"He won't be alive much longer."
 - Phlox and General K'Vagh

"It is more honorable to give one's life for medical research than to die for no purpose!"
"That choice is not ours to make!"
(General K'Vagh draws his weapon and shoots the subject)

"Proceed."
 - Antaak, Phlox, and K'Vagh

"I'm being compromised, sir, and I don't like it."
"Then I suggest you adjust your comfort level, Lieutenant."
 - Reed and Harris

(Translating Marab)" 'I have nothing to say to you, Human...' "
"That sounds like..."
"Klingon!"
"There must be some kind of mistake... according to his bio-signature, he is Klingon."
 - Sato, Archer, and T'Pol, making a startling discovery

"I've seen these sequences before – six months ago, to be precise. This is Augment DNA!"
 - Phlox, to Antaak and K'Vagh

"If you hope to ever leave this place, I suggest you stop asking questions and resume work."
 - K'vagh, to Phlox

"Is it unusual to have weird dreams after a mind meld?"
"Subconscious thoughts are often exchanged. They sometimes surface during sleep."
"I had a bizarre dream last night. Commander Tucker was in it. We were in a strange place – it was all white. There was almost a, uh... romantic quality to it. I don't ever remember dreaming about Commander Tucker before."
"Most unusual."
 - Hoshi Sato and T'Pol

"Your word isn't worth a lot at the moment."
 - Captain Archer, to Lieutenant Reed

"Perhaps you should've abducted Dr. Soong! He could have mapped this genome more efficiently than I can."
"We tried. Soong was under heavy guard."
 - Phlox and Antaak

"Why're you here?"
"That's a long story."
"Entertain me."
 - Marab and Reed

"You're fortunate to be alive. A Klingon who betrays his captain would be immediately executed."
 - Marab, to Reed

Background information

Story and script 
This episode and the following one () attempt to explain the makeup change in Klingons between TOS and , which had been semi-acknowledged as canon since the broadcast of DS9's  and  in the 1990s. Some viewers had criticized the Star Trek: Enterprise producers for not depicting Klingons of this era as smooth-headed, as they had been in the Original Series. While some fans simply ignored the Klingon makeup changes in the various series and films, others had longed for an "official" explanation. The writers of Enterprise hoped their take would find a way of satisfying both points of view, while simultaneously telling an interesting story. (For more from teleplay writer Mike Sussman, see Klingon augment virus.)
The final draft script of this episode was submitted on .

Continuity 
The mention of the Hur'q is a reference to the DS9 episode , where Worf, Jadzia Dax and Kor find the Sword of Kahless among the ruins of the Hur'q civilization in the Gamma Quadrant.
"Affliction" features the first appearance of the Rigelians in Star Trek. They, like the Tarkaleans, had been mentioned but not seen in previous series.
This episode is the first to bring Section 31, a concept introduced in , into Enterprise. Although the name "Section 31" is never mentioned in this or subsequent Enterprise episodes (though in the next episode, "Divergence", Agent  invokes "Article 14, Section 31" of the Starfleet Charter to justify his actions), interviews with the production staff confirm that this is indeed the same organization that was introduced in Deep Space Nine.
When asked why he's in the brig, Reed tells Marab that it is a "long story" – the same phrase Worf used 114 years later to describe the affair in .
Captain Hernandez makes her second appearance after . Also, Commander Collins references the xenophobic attack which took place in that episode and Trip mentions the Vulcan fire plains that T'Pol showed him in "Home".
Arik Soong is mentioned several times, as are the Augments which he genetically engineered.
Archer mentions Lieutenant Reed's father, Stuart Reed, who was seen in .
The Klingon augment virus was created as a result of the Human Augment DNA modifying the Levodian flu virus. In , The Doctor programmed himself with a simulated version of the Levodian flu at Kes' request to make him more sympathetic to his patients.
A reverse image of the Great Lakes was used in one shot of the Enterprise orbiting the Earth, apparently the same shot used to represent Kreetassa in A Night in Sickbay. This is puzzling as of course the image should not have been reversed; the image also seems to lack any other nearby water features actually present on the Earth, such as the St. Lawrence Seaway.

Sets 
The bridge plan for the Columbia duplicates that of the alternate Enterprise from .

Props 
A Klingon hypospray used in this episode, which was previously a Cardassian and Ferengi hypospray in  and  respectively, was sold off on week 4 of the It's A Wrap! sale and auction on eBay for $1026.

Cast 
Marc Worden previously played Worf's son Alexander in two episodes of .
Brad Greenquist previously played Demmas in  and Krit in 
Rivers is played by Family Guy creator Seth MacFarlane, who also made a brief cameo appearance in .
This episode marks the first appearance of Derek Magyar as Commander Kelby, who later appears in  and . His  also appeared in .
Kate McNeil, who plays Commander Collins previously worked with Scott Bakula on Bakula's show, Quantum Leap.

Trivia 
Close-ups of Lieutenant Reed's tactical console display references of 47.
The names of K'Vagh and Marab are not revealed in this episode and are derived from the script. General K'Vagh's name is also mentioned in the concluding part of this Klingon story arc, .
The Klingon dialogue heard in this episode was translated by Marc Okrand, the author of The Klingon Dictionary and many other works on the Klingon language. Okrand created the Klingon dialogue for several of the Star Trek feature films. Okrand was consulted by episode writer Mike Sussman, who wanted the characters to speak authentic Klingon.
This episode features the first named targ in Star Trek, Boshar (counting neither Toby the Targ, B'Elanna Torres' stuffed toy targ, nor Piggy, Molly O'Brien's stuffed targ).
The Enterprise reaches a new record top speed in this episode, warp 5.2.
The CGI model of Qu'Vat Colony is a slightly modified reuse of the digital model created for Zobral's encampment in the first season episode .

Reception 
Manny Coto cited this episode as one that "really turned out great." (Cinefantastique, Vol. 37, No. 2, p. 41)

Links and references

Guest Stars 
 John Schuck as Antaak
 James Avery as K'Vagh
 Ada Maris as Hernandez
 Eric Pierpoint as 
 Terrell Tilford as Marab
 Kate McNeil as 
 Brad Greenquist as a Rigelian Kidnapper
 Derek Magyar as Kelby

Co-Stars 
 Marc Worden as Klingon Prisoner
 Seth MacFarlane as Rivers

Uncredited Co-Stars 
 Adam Anello
 Michael Bailous as Klingon Assistant
 Jorge Benevides as R. Azar
 Solomon Burke, Jr. as 
 Paul Caroul as Klingon Augment
 Shawn Crowder as B. Cotton
 Thomas DuPont as Rigelian Kidnapper #3
 Jeremy Fry as MACO Private
 Glen Hambly as operations ensign
 Scott Hill as Hutchison
 Terita Jackson as Columbia helm ensign
 Roy Joaquin
 Ricky Lomax as W. Woods
 Andrew MacBeth as E. Hamboyan
 Dorenda Moore as S. Money
 Melissa O'Keeffe
 Ator Tamras as A. Tamras
 John Wan
 Aaron White as R. Ryan
 Brian J. Williams as Rigelian Kidnapper #2
 Wanda Willis as W. Willis
 Unknown performers as 
 Biggs
 Pierce
 Strong
 Enterprise MACO
 Klingon guards

Stunt Double
 Diana Lee Inosanto as stunt double for Linda Park

References 
2149; access tube; antimatter flow regulator; antiviral agent; assault; atmospheric residue; Augments; avenue; ; bio-sign; biosignature; black box; boarding party; Boshar; career; caste; cell rate; chef; Columbia; Columbia chef; com officer; command protocol; commutation; counts per minute (cpm); court martial; cranial ridge; data recorder; death sentence; Denobula; Denobulan ambassador; Denobulans; dilithium matrix; Director of Xenobiology; disruptors; dissection; DNA; dozen; drydock; Earth; emotional suppression; ENC ratio; encryption; engineering department; euthanasia; Fire Plains; frequency; Gardner; genome sequencer; going-away party; hadron; hadron count; Hur'q; IME; IME Conference; inferior species; intermix chamber; ion trace; Jennings; katra; kidnapper; kidnapping; Klingons; Klingon Augment starship; Klingon Empire; Klingon High Council; Klingon Imperial Fleet; Klingon magistrate; Klingonese; lab assistant; leverage; Levodian flu; MACOs; "Madame Chang's"; magistrate; Mazarites; metagenics; microdyne coupler; micron; mind meld (aka "meld"); N'Vak; N'Vak Colony; neural activity; neural pathway; North Maple Street; nucleotide; Orions; particulate remnant; patient; parts per million (ppm); perimeter scan; protein sequencing; Proxima colony; proximity scan; pulse; quartermaster; Qu'Vat Colony; recursive algorithm; ; Republic;  respiration; Rigelians; Rigelian language; ; Royal Navy; San Francisco; satellite grid; satellite log; Section 31; security clearance; sense of humor; sensor log; shore leave; ; Spacecraft Operating & Management System; Starfleet Charter; Starfleet Operations (aka Starfleet Ops); Starfleet Operations satellite (); Starfleet Security; subepithelial scan; Surak; surgically altered; systems monitor; tactical alert; targ; technical manual; test subject; Tiburon; transfer request; translation matrix; transporter; Vulcans; mind meld; warp field specialist; warp matrix; warp signature; warp trail; weapon signature; white; xeno-biology; Xindi mission

Columbia dedication plaque references 
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; Deep Space Operations; ; ; ; ; ; ; ; ; ; Earth; ; ; ; Environmental Systems; ; ; ; ; Flight Software; Flight Test Crew; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; Latin language; ; ; ; ; ; ; ; ; ; ; ; Mission Operations; ; ; ; ; ; ; ; ; Orbital Ergonomics; ; ; ; ; ; ; ; Propulsion Systems; ; ; ; ; ; ; ; ; ; ; ; ; San Francisco; ; ; ; ; ; ; Spaceframe Engineering; Starfleet Command; ; ; ; ; ; United Earth Space Probe Agency; ; ; Vehicle Development; ; Virgil; ; ; ; ; ; ; ; ;

External links 
 
 
 

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ja:ENT:クリンゴンの苦境
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ENT episodes