The Enterprise has mere minutes until a warp core overload destroys the ship. This was thanks to the sabotage inflicted by the Klingons, whom only one of which were captured. Captain Archer calls upon Columbia to give assistance.
Commander Tucker is the only one that can purge the computer of the sabotage but cannot beam aboard Enterprise while at warp. Columbia and Enterprise merges warp fields so a physical transfer of Tucker via a cable can be done. Lt. Reed is released from the brig to assist in the transfer.
After Tucker is safely aboard Enterprise, Reed is taken back to the brig. This leaves Tucker with a questioning look on his face. Soon enough though, Tucker is in Engineering with T'pol and working on the problem. Normally to purge the system would take time and that is a luxury they do not have. Tucker does a total shut down of the computer which requires Columbia to extend her warp field completely over Enterprise.
The strain on Columbia is great but Tucker manages to purge the system and restart the engines in time. Tucker decides to stay aboard Enterprise till the engines are fully repaired.
While the events upon Enterprise are going on, Dr. Phlox continues to work with Dr. Antaak in finding a cute for the Augment Virus. Phlox refuses to fix the problem with the augmentation of the Kilingons but thanks to Antaak, finds a way to stop the virus from causing further harm.
Back on Enterprise, Archer has discovered the source of Reed's betrayal and questions him about Harris. Reed is guilted to explain as much as he knows about Harris and the organization he works for.
General K'Vagh has been notified of Enterprise's supposed destruction and death of his son. With all he has went through, the Klingon High Command has decided to end the research and kill any colonies that hold Klingons with the virus. This comes right at the time that Phlox has found a way to stop the virus, but the orders have been given.
Back on Enterprise, Archer gets an unexpected message from Harris and information on where to find Phlox. After a brief conversation about Reed, Harris implies to the captain that entire worlds are at stake and that Reed should not be the focus here.
Soon however, Archer brings Reed to his ready room and talks to him about where his loyalties lie. Reed tells the Archer he doesn't know where Phlox is but that Starfleet does know where a Klingon colony is that does genetic research. Soon after, the Enterprise sets course for the colony and Reed is brought back to duty.
Phlox is experimenting upon the willing Klingons in the hope of narrowing down the right sequence for a cure. The findings are good but he is working against the clock. Just then Archer arrives and beams upon the Klingon ship to rescue Phlox. But in an astonishing confession, Phlox lets his true motives out. He is working on a cure for the virus and not a way to continue the augmentation. Phlox has no intention of leaving till his work is done.
However the work is going to slow to narrow the cure down. They need human DNA to hurry the process along since the virus originated among human augments. Archer volunteers and is infected with the virus. As ridges form upon his forehead, Phlox is able to narrow the results and find the cure.
After a near battle with a Klingon destroyer bent on destroying the colony of infected Klingons, the cure is given out. The results are a more human look to the infected Klingons but very little else. Everyone is back where they need to be and Enterprise leaves the system. Reed takes a moment and contacts Harris, telling him not to contact him ever again.