Enterprise has returned to Earth for the launch of the Columbia. While Trip prepares for his transfer, Hoshi and Phlox enjoy dinner in San Francisco. Things turn sour, however, when Phlox is kidnapped by mysterious aliens and taken to a Klingon laboratory on the colony world of Qu'Vat. Dr. Antaak and General K'Vagh inform him that a virus is spreading through the Klingon Empire — they need Phlox's help to devise a cure.
On Enterprise, T'Pol mindmelds with Hoshi, hoping that the ensign will remember something about Phlox's kidnappers. The duo manages to deduce that the kidnappers were speaking Rigelian, so Enterprise takes off after a recently departed Rigelian vessel.
On the Columbia, Trip has dinner with his new captain, Erika Hernandez. Erika is surprised that Trip accepted a transfer, and Trip simply says that he was getting too close to some of his Enterprise crewmates — sometimes it's easier to work with people who are merely colleagues. Back on Enterprise, T'Pol has a strange meditation session in which she sees and interacts with Trip. On Columbia, Trip appears to have the same vision.
Meanwhile, Reed is approached by a mysterious man named Harris, who has an assignment for him. Reed balks, since the assignment will mean deceiving Archer, but Harris insists it may be the only way to save Phlox.
Archer and the crew eventually find the Rigelian vessel, but it's been destroyed and there are no survivors. Suddenly, Enterprise is attacked by a small, mysterious vessel. A group of fierce, human-like aliens board the ship and interfere with Enterprise's systems. One of their boarding party, Marab, is hit by MACO fire and is left behind as the rest of the aliens flee. Archer wants to follow the strange ship, but Enterprise's systems appear to be disabled. In Sickbay, Archer asks Marab why his people attacked Enterprise. Strangely enough, Marab responds in Klingon — and according to his bio-signature, he is Klingon. The crew isn't sure what to make of this, but in the meantime, Archer asks T'Pol and Hoshi to reconstruct data recovered from the Rigelian ship.
On Qu'Vat, the Klingons bring Phlox a Klingon specimen for dissection — the "specimen," however, is still alive. Phlox notices that the specimen 's skin appears to be peeling, his forehead ridges smoothing out. Despite the doctor's protests, K'Vagh kills the ailing Klingon, giving Phlox something to study. As Phlox works, he discovers something disturbing — his specimen has Augment DNA.
Phlox realizes the Klingons were attempting to create Klingon Augments. Unfortunately, there were some unanticipated side effects, and the Augments' forehead ridges began to dissolve. Antaak says that it seemed for a while as if the experiment was successful — the Klingon Augments looked human, but were still very Klingon in nature. Then their neural pathways began to degrade and they died in agony. One of the Klingon test subjects happened to be suffering from the Levodian flu — the Augment genes modified the virus and it became airborne, resulting in the current plague.
Back on Enterprise, Archer has discovered that Reed lied to him. Reed erased important information pertaining to the Rigelian ship and claimed the ship was destroyed by Orion weapons. T'Pol, however, tells Archer it was actually destroyed by Klingons. When Reed refuses to tell the captain what's really going on, a furious Archer confines him to the brig.
On Qu'Vat, Phlox and Antaak are running out of time. K'Vagh tells them they must devise a cure in five days. Phlox insists this is impossible, so Antaak proposes an alternate solution: successfully create Klingon Augments and figure out a way for them to survive. The Augments could be used as leverage and the High Council would be forced to give Antaak and Phlox more time to find a cure. Phlox, however, refuses to assist in this experiment.
Meanwhile, Enterprise is experiencing difficulties, having been sabotaged by Marab and the other altered Klingons . The only way to keep the warp reactor from breaching is to increase speed. Desperate, Archer orders Mayweather to take the ship to warp 5.2 — faster than Enterprise has ever gone before.