At the end of "
Cold Station 12", Doctor
Arik Soong and the Augments he secretly raised depart the space station, taking with them 1,800 frozen Augment embryos preserved from the time of the
Eugenics Wars. Malik also steals pathogen samples from the station and sets the containment fields to fail. In "The Augments", Captain
Archer restores stasis around the central compound, and is beamed from space to safety. He takes the
Enterprise in pursuit of Soong, Malik, and the Augments in their stolen
Bird of Prey. Soong and the Augments arrive in
Klingon space where he shares his plan: Soong intends to hide out in a region (the
Briar Patch) where Starfleet would have trouble tracking them down. Malik objects to Soong's plan, noting that
Khan Noonien Singh also ran away on the SS
Botany Bay. In pursuit of the Augments
Enterprise arrives in Klingon space, having faked a Klingon
warp signature. Soong releases a hostage on a Denobulan shuttle into a gas giant, forcing
Enterprise to abandon the pursuit and mount a rescue operation. Escaping, Malik proposes a new plan: trigger a war between Starfleet and the Klingons as a distraction by firing a pathogen-filled torpedo at a Klingon colony. He reasons that Starfleet will be too busy fighting the Klingons to hunt down the Augments. Soong will have nothing to do with Malik's genocidal proposal. On the
Enterprise, Commander
T'Pol asks Commander
Tucker about the distance between them after her recent arranged marriage. He tells her he has come to terms with their new relationship. Back on the Bird of Prey, Soong works on a way to remove aggressive behavior from the unborn Augment embryos. Malik, concerned by Soong's plan to hide from Starfleet and his tampering with the embryos, leads a mutiny which confines Soong to his quarters. With the help of Persis, Soong leaves the ship in an escape pod.
Enterprise, once again in pursuit, detects the pod and brings Soong on board. Heading towards the Klingon colony at high warp in an attempt to stop Malik's plan, the Klingons detect their ship.
Enterprise is forced to disable a Klingon cruiser when it tries to board. Malik kills Persis for her betrayal, and continues with his plan to attack the Klingons. Scans of the ''Qu'vat'' colony reveal three main population centers; the torpedo is armed with pathogens and prepared for deployment. The
Enterprise arrives at the ''Qu'vat
colony just after Malik fires the torpedo, but Enterprise
destroys it, saving the population. Soong helps disable the Klingon ship, hoping to save some of the Augments. However, Malik scuttles the Klingon ship, killing the remaining Augments and the embryos; and transports himself onto Enterprise'' in an attempt to kill Soong in revenge. Archer manages to kill Malik first, blowing a hole clear through him. The Klingons call off their retaliation against Earth, and Soong is returned to the Starfleet Detention Center. In custody, he begins to doubt the feasibility of genetically engineering humans; and wonders if perfecting
artificial life holds better possibilities for the future. ==Production==