“Affliction” is episode fifteen of season four of Star Trek: Enterprise.
A Klingon is bundled into a room by others and strapped into a chair, then linked to an IV. He says his death sentence was commuted. When the IV starts, his cranial ridges start smoothing out.
Enterprise has arrived home for the official launch of Columbia. In the previous episode, “The Aenar”, Trip asked to be transferred to Columbia. He’s looking at her in spacedock from his quarters when T’Pol enters. He asks if she’s coming to his going away party in the mess hall. She doesn’t understand the logic of the transfer; he isn’t being promoted and wouldn’t leave the captain without sufficient reason. Trip says it’s the challenge of getting a new ship into shape. She asks if he’s leaving because of her. Despite Trip’s non-answer then answer, more than likely.
Phlox and Hoshi are leaving a restaurant he likes that has become a lot busier, thanks to Hoshi, when they are accosted by three people. They fight, Hoshi gets knocked down and Phlox stunned and bundled away.
Captain Archer arrives and is filled in by Reed, Hoshi and Commander Collins of Starfleet Security. Hoshi says she heard one of the attackers say something that wasn’t English, but she doesn’t know what language as it was just before she passed out. Collins reports that only Phlox and Hoshi’s DNA is at the scene, and a residual trace which Reed thinks could be from a transporter. Collins seems to think that’s unlikely. She references Phlox’s confrontation in “Home”; Reed does not think it’s connected. When Collins leaves, Archer tells Reed to check the satellite logs for any transporter activity.
Trip is in Columbia‘s engine room filling his new crew in on what he wants; they were supposed to have launched 6 months ago. Captain Hernandez joins him after; it’s customary to report to the captain. Trip apologises; he wanted to know what the situation was like first. She invites him to join her in the captain’s mess.
T’Pol enters the captain’s ready room. Nothing has been heard from Phlox’s kidnappers. Archer suggests T’Pol do a mind meld with Hoshi to help her remember. T’Pol has never initiated a meld before; she lacks the proper training. That’s okay; the captain can walk her through it. He had Surak’s katra in his head for four days and picked up a few things.
Reed is checking the satellite logs, but there’s no data. He contacts Starfleet Operations, only for the hail to go elsewhere. The man, who Reed knows, tells Reed to meet him at an address in an hour.
T’Pol performs the mind meld and Hoshi recognises the language as Rigellian. A Rigellian freighter left orbit after the abduction, and its flight path does not match its flight plan.
Reed meets the man he spoke with. He wasn’t aware he was still part of the other’s section. Reed is told there’s a job that needs doing and this may be the only way to save Phlox’s life.
Phlox is with some Klingons. He is introduced to a Dr Antaak, who he will be working with. Or he will die. Phlox thinks there are easier ways to recruit a new lab assistant. He’s told that Antaak will be assisting Phlox, not the other way around. Antaak saw Phlox at an IMU conference five years ago. He was disguised as a Mazarite, as Klingons were not invited. The other, General K’Vagh, expects a progress report by sunrise and leaves.
Antaak apologises for the general’s behaviour. The Empire is facing its greatest threat since the Hur’q Invasion. There’s a virus that’s spreading and millions are affected. If it continues, the Klingon species will die. The Klingons didn’t ask for help, as that looks weak and may incite rebellion. It wasn’t Antaak’s idea to abduct Phlox, but he’s here and millions of lives are at risk.
Enterprise is following the freighter. Trip’s replacement isn’t as good as him. Trip dines with Hernandez; it seems some of his people already want to leave his department. She denied the requests. Trip says he was a little too comfortable on Enterprise; sometimes it’s easier to work with people who are colleagues not friends.
Reed is hiding stuff from Captain Archer, presumably on orders from the man he met. Trip ends up inside one of T’Pol’s meditation trances. Phlox discovers something about the virus affecting the Klingons. The story continues in the next episode, “Divergence”.