When genetically engineered humans left over from the Eugenics Wars hijack a Klingon ship, the Klingons threaten war with Earth. Archer enlists the criminal Dr. Arik Soong, the Augments' creator and "father," to help hunt them down.

The Enterprise crew cautiously pursues Dr. Arik Soong and his superhuman Augments across hostile Klingon space toward a hidden planet where he intends to raise his Augment army. But in defiance of their "father" Soong, Malik devises a heinous plot to use a bioweapon against a Klingon colony planet, undoubtedly leading to interstellar war, to safeguard the Augments from Enterprise and further Starfleet interference. Malik's rash proposal leads to a rift with Soong.