In Enterprise's brig, Archer briefs Reed on the situation: the Klingons altered the ship's engineering subroutines and if Enterprise drops below warp 5, the reactor will explode. Archer has a plan to bring Trip aboard from Columbia, but he needs Reed's help.
Enterprise and Columbia, both flying at breakneck speed, get into formation. Reed deploys a cable from Launch Bay 2, which Trip uses to maneuver from one ship to the other. Once onboard, Trip sets his plan into action, shutting down Enterprise's warp reactor and purging the subroutines. Enterprise moves inside Columbia's warp field in order to maintain speed. The plan is risky, but it's a success — Enterprise is back in working order.
On Qu'Vat, Antaak approaches Phlox, who is barely conscious after being badly beaten. After reviewing Phlox's research, Antaak believes the doctor has discovered a weakness in the virus that's causing the plague among Klingons. There may be a way to stop the genetic effects of the virus in the early stages, meaning there will be changes in the affected Klingons' appearances, but no further developments, such as enhanced strength and speed. This means that Phlox and Antaak should be able to cure the virus, but it will not result in the Klingon Augments K'Vagh wants. Antaak suggests that he and Phlox simply keep that part a secret from K'Vagh. Realizing that this may be the only way to find a cure, Phlox agrees.
Meanwhile, the metagenic Klingons who boarded Enterprise report to K'Vagh. Their leader, Laneth, tells K'Vagh that Enterprise was destroyed and Marab — who is K'Vagh's son — was killed by humans. K'Vagh storms into the lab and asks Phlox and Antaak for an update. Phlox says that he is close to perfecting the Augment genome — but he needs more time.
On Enterprise, Archer has discovered Reed's communications with the mysterious Harris and orders Reed to send Harris a message. Later, Harris contacts Archer. He tells the captain that Phlox must complete his assignment and find a cure. If Archer tries to interfere, the after effects will have grave implications for entire worlds. Reed apologizes to Archer for his deceit, revealing that he became a part of covert operations when he was just an ensign, and thought his involvement was over. The lieutenant decides that his loyalties lie with Archer: he tells the captain that Starfleet Intelligence believes the Klingons have a genetic research facility on Qu'Vat Colony.
On Qu'Vat, Phlox works furiously, racing against time. Under K'Vagh's orders, he infects K'Vagh, Antaak, and two Klingon guards with different strains of the virus to figure out which one holds the cure. Suddenly, Archer and Marab burst into the lab. Archer and K'Vagh argue, but Phlox interrupts: he only needs a little more time to find a cure for the plague. K'Vagh is angry that Phlox lied about working on the Augment genome, but Phlox points out that finding a cure is the only way to keep Marab from dying.
Unfortunately, Phlox is running out of time faster than he bargained for: Fleet Admiral Krell and his ships are approaching, and they're prepared to wipe out Qu'Vat colony. Enterprise and Columbia do their best to hold the Klingon ships off while Phlox continues to work. Phlox notes that there is a way to speed up the process — he needs a human host to replicate antibodies and finish the antivirus. Archer volunteers.
The plan works and, as Archer screams in pain, his forehead rippling, Phlox collects a sample of the cure. He then has Antaak transport a potent sample of the metagenic virus to Krell's ship — if Krell powers down his weapons, Phlox will give him the cure. Krell deems this a cowardly attack, but in the end, he has no choice but to stand down. The Klingon High Council agrees to distribute the cure throughout the Empire.
Onboard Enterprise, Phlox examines Antaak. After being infected with the virus, the Klingon doctor's forehead ridges have completely disappeared — he has become a metagenic Klingon. Antaak is a bit disturbed and notes that millions of Klingons will have to live with this cosmetic change, which will be passed down to their children. Ever hopeful, Phlox tells him that it may be possible, in the future, to reverse the effects. Moved by his new friend's help, Antaak thanks Phlox.
Meanwhile, Harris contacts Reed once more. The lieutenant is firm, however — he bluntly tells Harris to never contact him again. Reed says that from now on, he only answers to one commanding officer — Jonathan Archer.