Malik overthrows Soong and fires a pathogen-armed torpedo at a Klingon colony to provoke a war, while Archer races to stop him.
Soong wants to hide the Augments and secretly tries to remove aggression from the embryos, but Malik plans to start a war by attacking the Klingon colony at Qu'vat with a pathogen. Malik takes control and confines Soong, who escapes with help from Persis, whom Malik then kills.
Enterprise destroys the torpedo before it can strike the colony. Malik scuttles his ship, killing the remaining Augments and the embryos, then beams aboard Enterprise to kill Soong, but Archer kills him. Back in detention, Soong begins to think artificial life may hold more promise than genetic engineering. The episode was directed by LeVar Burton and written by Mike Sussman.