Klingons kidnap Phlox to cure a plague created by an experiment to give Klingons Augment traits, as Enterprise investigates his disappearance.
Enterprise returns to Earth for the launch of Columbia, where Tucker is transferring. In San Francisco, Hoshi and Phlox are attacked and Phlox is abducted. Reed receives a secret assignment from a mysterious agent, later revealed as part of Section 31, and Archer confines him to the brig for tampering with evidence. T'Pol performs her first mind meld, with Hoshi, which points to a Rigelian ship, and later shares a vision with Tucker while meditating.
On the Klingon colony Qu'Vat, Phlox learns from Doctor Antaak that Klingon experiments with Augment DNA after Borderland have produced a mutating plague, which Phlox has five days to cure, and he refuses to help create stable Augment Klingons. Boarders sabotage Enterprise, which must race at warp 5.2 to avoid a core breach. This first half of a two-parter concluding in Divergence explains why Klingons look human in the original series. Mike Sussman wrote the teleplay from a Manny Coto story.