With a deadly pathogen about to be released, Captain Archer barely makes it back to the Enterprise
. His goal is now to track down the Klingon Bird-of-Prey and stop Dr. Arik Soong and the Augments from finding a location to raise thousands of Augment embryos.
Back in the Bird-of-Prey, Malik starts to question Dr. Soong's judgment when Soong wants to change the embryos' DNA to make them less violent and more human. Malik defies Soong's orders and takes leadership of the Augments. His goal is to create a war between the Humans and Klingon which would enable the Augments to grow in power. Soong realises his place is no longer with the Augments, and seeks to find an escape route off of the Bird-of-Prey. He realises that the only way he can stop Malik's plan is to join forces with Captain Archer.