A Klingon scientist is working, while being watched by soldiers. Two more soldiers lead a Klingon prisoner into the lab, and the prisoner claims that his death sentence was commuted and demands to talk to the magistrate who presided over his trial. The soldiers strap him to a chair and give him an injection, which causes his cranial ridges to disappear.
Enterprise visits Columbia in drydock, with the intention of assigning Trip to Columbia. While Trip is packing and admiring the new ship out the window, T'Pol enters. He invites her to a "going away party", but she simply admits to being confused about his departure. He explains that the new assignment is more challenging and she leaves.
In San Francisco, Phlox and Hoshi leave a restaurant, with Phlox noting that he was offered a job at the Interspecies Medical Exchange as a Doctor of Xenobiology, and he's considering the offer, but doesn't want to say goodbye to his friends. Three men appear out of an alley and order Phlox to go with them, threatening them with a disruptor. Hoshi tries to fight back, but she's knocked down and rendered semi-conscious. Phlox is stunned and taken away, and Hoshi hears the men talking in an alien language.
Archer and Malcolm visit the crime scene and meet a Starfleet security officer called Commander Collins. Collins informs Archer, Malcolm, and Hoshi that the only DNA found belonged to her and Phlox, but there were some ionization traces nearby, causing Malcolm to suspect that they beamed away. Collins explains that most people don't possess transporters that leave ionization traces and wonders if the men were working for the guy who attacked Phlox a few months ago. However, Malcolm believes that that guy was too stupid to think of such a complex plan. Collins leaves to investigate further, and Archer orders Malcolm to check if the Starfleet Operations satellites detected any transporter activity at the time of Phlox's abduction.
On Columbia, Trip tells the other engineers to do various engineering tasks, then Captain Hernandez enters. She reminds him that assigned officers generally report to their captains on arrival and invites him to dinner. She then asks him to have his uniform patch changed.
T'Pol enters Archer's ready room and tells him that Phlox's wives now know of his kidnapping. Archer, knowing that Hoshi heard the three men talking, asks T'Pol to mind meld with her, with him (having had experience with Surak's soul) guiding her. In the armory, Malcolm finds out that the satellite grid was off-line for maintenance at the time of the kidnapping. He contacts Starfleet, but there's no reply, then a man appears onscreen. He, whose name is Harris, claims that he will tell Malcolm why the satellite grid was down if he meets him at an address in San Francisco.
T'Pol, after a bumpy start, manages to mind-meld with Hoshi, who realises that the three men were speaking Rigelian. T'Pol enters the bridge and tells Archer that a Rigelian freighter did leave Earth about two hours after Phlox's abduction, and that it was scheduled to arrive at Proxima colony but scans suggest it went elsewhere. Archer orders T'Pol to return all crew to Enterprise, then leaves to contact Admiral Garner.
That night, Malcolm meets with Harris in San Francisco. It turns out that Harris was responsible for the grid shutting down and he works for a section that needs Malcolm's help (also implying that Malcolm used to work for said section himself) or else Phlox may die.
In the laboratory, the Klingon general K'Vagh watches the scientist make a vial of green liquid. Phlox is led into the lab, where K'Vagh warns Phlox that he will be put to death if he doesn't cooperate with the scientist, whose name is Dr. Antaak. Antaak recognises Phlox from a conference, which he attended incognito. K'Vagh leaves, demanding a progress report by sunrise the next day. Antaak reveals that the Klingons are dealing with a very dangerous plague, and that they didn't ask for Starfleet's assistance since they thought that was cowardly. Thus, the two doctors start working on researching the virus.
Meanwhile, on Enterprise, T'Pol loses the freighter's warp trail, causing Archer to suggest that they dropped to impulse. He tells Commander Kelby to speed up the ship. On Columbia, Trip and Hernandez are dining together, and she reveals that two unspecified engineers requested transfers, which she turned down. He tells her that Columbia is almost ready for warp trials, and she asks him what made him want to change ships. He responds that sometimes he prefers to work with people who he doesn't consider his friends.
T'Pol meditates, and sees a white void with Trip in it. She tells him to leave, but it turns out that he's trying to daydream and they're psychically linked. Ensign Rivers then snaps Trip out of his daydream by handing him a padd. Meanwhile, Archer calls T'Pol to the bridge since the ship is nearing the freighter's coordinates.
On the bridge, the viewscreen displays wreckage of the Rigelian freighter. T'Pol confirms that its crew are dead and there were no Denobulans. Archer asks Malcolm to determine the freighter's destroyer, and he can, but he lies to Archer that he can't. Archer, who is none the wiser, tells Malcolm to scan for the ship's data recorder.
On Qu'Vat Colony, Phlox believes that the virus is a variant on Levodian flu and suggests contacting the IME. Antaak doesn't believe they need them, however, as they stole their medical database, leading to an ethical debate about stealing. K'Vagh returns with another prisoner, who Phlox confirms is infected. He worries that the prisoner will infect him and the others, but Antaak assures him that the infection only becomes contagious when it's in a later stage. Antaak tries to euthanise the prisoner by shooting him, but Phlox stops him. They argue, but then K'Vagh shoots the prisoner to death himself, shocking both doctors.
Malcolm contacts Harris in his quarters, frustrated that the section destroyed the Rigellian freighter, and asks who was on board, but Harris refuses to reply. Malcolm reveals that he has analysed the weapons signatures and is keeping the information secret, but is unsure how long he can keep the secret for. Harris tells a reluctant Malcolm to lie that it was Orions that destroyed the ship, then, the Enterprise becomes under attack, necessitating that Malcolm leave.
A Klingon ship fires at the Enterprise, while Malcolm arrives, and T'Pol notes that the Klingons aren't responding to Hoshi's hails. Archer orders Malcolm to fire at the Klingon ship. Klingons without cranial ridges beam aboard Enterprise and run through the corridor into an access tube. When Hoshi catches them, Archer tells Malcolm to seal the access tube and deploy a team of MACOs. They arrive and fire at the Klingons. One of them, Marab, fires back, but doesn't hit anybody. Marab orders his ship to fire at the MACOs, so the warship thrashes the Enterprise and causes an explosion where the MACOs are, forcing them to retreat. Archer orders Malcolm to disable the ship.
The Klingons finish their work and prepare to leave, but Marab is shot by a MACO, who is shot with a disruptor. When more security shows up, the boarding party flees, leaving Marab behind. Travis tries to pursue them, but the helm station is offline. Archer questions Marab in sickbay, where T'Pol and Hoshi are surprised that he's Klingon as he has no ridges.
Later, Archer, T'Pol, Malcolm, Hoshi, and Travis gather on the bridge to speculate. Malcolm wonders if Marab had surgery to disguise himself as a human, while T'Pol determines that the repair work will take six hours. Archer orders Travis to help Kelby analyse the damage. T'Pol then reveals that the Rigelian freighter's data has been deleted, so Archer orders her and Hoshi to attempt to restore it.
On Qu'Vat Colony, Anaak's targ Boshar chews on Phlox's clothes, and Phlox finds Augment DNA in the virus. K'Vagh explains that they couldn't allow the human Augments (two of whom boarded a Bird-of-Prey earlier) to provide Starfleet with an advantage. Phlox argues that genetic engineering is now illegal in Starfleet, but K'Vagh doesn't seem to care. Then Phlox, noting that the Augments are dead, wonders where the DNA is from, and K'Vagh explains that it came from some embryos they found. He also explains that the test subjects initially did get stronger and smarter, but they also became more aggressive, lost their cranial ridges, and later their neural pathways degraded, causing extreme pain and eventually death. Finally, he explains that the disease came from a test subject who had Levodian flu, which combined with the DNA and became airborne.
Back on Enterprise in the situation room, T'Pol suggests that Hoshi try using a recursive algorithm to reconstruct the Rigelian data. Hoshi asks if mind melds have side effects, and when T'Pol reveals that they can cause unusual dreams, Hoshi reveals that she also dreamt that Trip was in a strange white area. Furthermore, despite never having dreamt about Trip before and not having any romantic feelings towards him, her dream had a romantic aspect to it.
In Archer's ready room, he, T'Pol, and Hoshi determine that the data recorder's memory core was erased with a device called a microdyne coupler, which was found in storage locker C-14, which was last accessed by Malcolm. Archer calls Malcolm in for questioning, but Malcolm insists that the Orions did it. Archer reveals that T'Pol examined Malcolm's analysis and determined that it was Klingons instead, and demands an explanation, but Malcolm refuses to answer. Thus, Malcolm is relieved of duty and sent to the brig.
In the brig, Archer warns Malcolm that the Enterprise is headed into Klingon territory and asks if he knows where Phlox is, but Malcolm says he doesn't. Archer expresses disdain that Malcolm would betray him, but Malcolm says he isn't working for the Klingons. Archer asks who he is working for, but Malcolm doesn't reply.
Meanwhile, on Qu'Vat colony, Antaak is losing patience and reveals, to Phlox's horror, that the plague victims are being killed. Phlox reveals that he believes he can develop an antiviral agent, but it would take weeks, scaring K'Vagh, as he fears millions will be infected in that time. K'Vagh reveals that a fleet is on its way to Qu'Vat colony to destroy them, but Antaak has an idea— stabilise the Augments' DNA and use them to force the High Council into giving them more time to work. Phlox refuses to participate, so K'Vagh has soldiers take him away.
On Columbia's bridge, Hernandez, after checking with the dockmaster and the engineering staff, launches the ship. Meanwhile, on Enterprise, the brig has been divided into two and Marab placed in the second cell, who notes that Malcolm is lucky to be alive since Klingons get executed for lying to their superiors. Then, the ship starts to shake, which Travis determines is due to an increasing pressure of the warp plasma and the anti-matter flow regulators being locked open. He determines that if they dropped into impulse, the warp reactor would breach, but if they speed up, the pressure of the warp plasma would fail. Archer orders Travis to continue at maximum warp and T'Pol to assist the engineers.
In the brig, Archer, believing the Klingons caused the damage, demands Marab teach him how to fix it, but he refuses, even when told he would die if the reactor breached. Malcolm offers help, but Archer leaves, not listening. Meanwhile, T'Pol and Kelby find out that the Klingons did cause the damage, and they also interfered with the command protocols. T'Pol is unsure she can reverse the damage, but she promises to do her best. Travis reports that the pressure is still rising, prompting Archer to order him to increase speed to Warp 5.2, which he does...
Tropes in this episode include:
- Alien Abduction: While Phlox is an alien himself (albeit a different species than the Klingons), the Klingons also tried to abduct Soong, but failed because he was guarded.
- All Asians Know Martial Arts: Again, Hoshi (the only major Asian character on the show) is shown to know aikido.
- Blue-and-Orange Morality: Klingon and Denobulan medical ethics are clearly way outta sync, as demonstrated when Antaak has no problem euthanizing a sick man so Phlox can dissect his body, over Phlox's objections. K'Vagh then settles the issue by shooting the poor bastard.
- Call-Back:
- Commander Collins suggests that Phlox's abduction has something to do with the Bar Brawl from earlier in the season. Malcolm, however, dismisses that theory, as the guy from before was just a drunken idiot and not a criminal mastermind.
- Back in "Trials and Tribble-ations," Bashir and O'Brien wondered if the smooth Klingon foreheads were a result of a genetic experiment or a virus. Turns out they were both right.
- General K'Vagh explains to Phlox that the attempt to create Klingon Augments is a result of what happened during the Augment arc.
- In addition, Phlox says that the Klingons should have abducted Dr. Soong if they wanted faster results. Turns out, they tried that, but found he was under heavy guard.
- Seth MacFarlane (yes, him again) returns as an engineer aboard Columbia (possibly having transferred with Trip).
- Hoshi gets to demonstrate her black belt in Aikido that she mentioned just a few episodes earlier.
- Call-Forward: The Levodian Flu makes its reappearance after first being mentioned in the Star Trek: Voyager episode "Tattoo."
- Dark Secret: We learn something about Malcolm Reed that we never expected: he was a member of Section 31.
- Go Fast or Go Boom: The pressure built up by the warp plasma will blow up Enterprise if it doesn't continuously increase in speed.
- Honor Before Reason: Subverted by Antaak, who's willing to use underhanded methods when necessary.
- It's a Long Story: Malcolm telling his Klingon cellmate why he's in the brig.
- Klingon Scientists Get No Respect: We see just how poorly regarded Doctor Antaak and his profession are. Antaak gets even less respect than usual since he rejected tradition (his family is of the warrior caste) to become a doctor.
- Mindlink Mates: Trip finds himself in T'Pol's mental White Void Room. Neither is particularly happy about it.T'Pol: Why are you here?Tucker: I was about to ask you the same thing. Is this a daydream?T'Pol: I'm meditating. This is where I go in my mind.Tucker: Well, 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: Please leave.Tucker: Exactly where am I supposed to go?
- The Mole: Malcolm's CO in Section 31 asks him to be this.
- No, You: Trip's response to being told to get out of T'Pol's head.
- Plague Episode: Downplayed— the main conflict involves a serious Klingon virus, but no one important catches it since it won't become contagious until its third stage.
- Red Shirt:
- One bites it when the Klingons board Enterprise.
- Several MACOs get caught in an explosion, but it's not clear if they're killed or just slightly burnt.
- Scotty Time: Phlox says that he'll need weeks to cure the Augment plague, but he only has five days before the Klingon fleet destroys Qu'vat colony.
- Took a Level in Badass: Hoshi Sato, the nervous alien language specialist, demonstrates martial arts skills during Dr Phlox's kidnapping. While it's likely Hoshi would have become more assertive after her experiences during the Xindi conflict, it would have made more sense for her to have used the more simple takedowns taught to the crew by Major Hayes during this time. But less cool, of course.
- What the Hell, Hero?: Archer is very pissed at Malcolm for lying to him.
- You Have Outlived Your Usefulness:
- The Klingons kill the Rigelians who kidnapped Phlox.
- Phlox is threatened with execution if he doesn't cooperate, a fate he's willing to accept.
- Your Favorite: Trip's first dinner on Columbia with Captain Hernandez includes pecan pie.
