Trapped on Cold Station 12 with soon-to-be-released deadly pathogens, Captain Jonathan Archer barely manages to divert them before being transported back aboard Enterprise in the nick of time, narrowly escaping death. Now more than ever, Archer is driven to track down Dr. Arik Soong and the Augments in their hijacked Klingon bird-of-prey as they seek refuge in an isolated locale to "raise" thousands of just-begotten Augment embryos.
Aboard the bird-of-prey, Malik — who considers himself the Augments' true leader now — continually questions Soong's leadership. And Soong is shocked to learn that — instead of having their ship take them to a safe haven — Malik has designs on a far more diabolical plan. With pathogens he has purloined from Cold Station 12, Malik wants to unleash them aboard torpedoes aimed at the Klingons' Qu'vat colony. With the Klingons blaming humans on that ensuing tragedy, Malik knows a war would undoubtedly result which would keep Klingons and Starfleet embittered and embattled as the Augments rise to power. Conversely, Malik is upset to discover that Soong has decided to manipulate the DNA of the embryos to make them less violent. Malik realizes that Soong must have also fixed "mistakes" in his generation of Augments as well.
On Enterprise, Archer and his crew make headway in determining how to track down Soong and the Augments. But when Archer makes contact with them, Soong orders an attack, and their two ships engage in battle. Yet just as Archer feels that stopping Soong and his "offspring" is imminent, Soong waylays them by stranding a female Denobulan in a shuttle that he knows Archer will rescue. Even so, Archer pledges that he will see Soong again soon.
After their unexpected detour, Archer enlists the crew's expertise in pinpointing Soong's bird-of-prey once again. But trouble is brewing for Soong aboard his ship. Malik has corralled the other lead Augments — including Soong's favorite, Persis — in removing Soong from command and imprisoning him aboard the ship. Soong is hardly surprised, but also realizes that he must stop Malik's deadly plan: it will only prove what others say about the Augments and all the Augments will be killed as a result.
Persis helps Soong escape in a shuttlepod and he calls on his only option: a surprised Archer. Archer isn't convinced that the duplicitous Soong is actually on his side, even with his scenario that Malik has planned to attack a Klingon colony. But Soong is able to prove his case with evidence on the stolen pathogens. With that information, Archer has Soong work with the Enterprise crew on once again finding the Augments' ship and intercepting their fatal torpedoes.
Having discovered that Soong has escaped, Malik — who has sussed out Persis as his traitor and killed her — takes command of the bird-of-prey to attack the Klingon colony. Soon, he is engaged in trying to accomplish his deadly mission before Enterprise catches up with him. But the two are soon in battle as Enterprise succeeds in halting the torpedoes' course, and the Augments sustain massive injuries. However, this accomplishment only seems to embolden Malik further as he prepares to continue an assault on Enterprise. At that point, Soong pleads with Malik to stop and save his brethren. Shortly thereafter an explosion rips through the bird-of-prey, decimating it. However, Malik has escaped the ruin by transporting himself onto Enterprise, where he is bent on killing Soong, and proceeds to strangle him. Archer then saves Soong by shooting and killing Malik.
While Archer has afforded Soong some leniencay since he helped save the Klingon colony, the doctor must still return to jail, as Archer accompanies him to the Starfleet Detention Center. Despite Soong's last research ending so disastrously, he decides to commence other studies ... this time concentrating on artificial lifeforms.