The series follows the adventures of the first Starfleet starship Enterprise, registration NX-01. In this episode, genetically engineered Humans called "Augments" have captured a Klingon vessel, and Enterprise is sent to find them. They retrieve the Augments' creator, Doctor Arik Soong (Brent Spiner), and head in pursuit. The episode is the last of a three episode arc, preceded by "Borderland", and "Cold Station 12".
Captain Archer manages to restore stasis around the central compound, and is beamed from space as pathogens flood the compound. Arriving in Klingon space, Doctor Soong plans to take the Augments and the stolen embryos to an region flooded with radiation from supernova remnants, which he refers to as the "Briar Patch". It contains several habitable planets they could settle, and they would be difficult to locate within the clouds of radiation. However, Malik vocally dissents against what he sees as a weak and cowardly plan, preferring to create a distraction by triggering a Human-Klingon war instead.
As they work to enhance the sensors, Commander T'Pol asks Commander Tucker about the recent distance between them. Meanwhile, noting the aggressive tendencies of his "son", Soong begins working on a way to remove that behavior from the unborn Augments. Malik, concerned by Soong's tampering, leads a mutiny which sees him confined to his quarters. With the help of Persis, however, he leaves the ship in an escape-pod, which is soon detected by Enterprise. Malik kills Persis for her betrayal of him, and continues with his plan to attack the Klingons. Scans of the Qu'vat colony reveal three main population centers, and preparations are made to explode a torpedo armed with some of the pathogens stolen from Cold Station 12 into the atmosphere.
Enterprise arrives and manages to destroy the torpedo, then proceeds to disable the Klingon ship after Soong tells Archer where the stolen warship is most vulnerable. Malik prefers to die rather than be captured and proceeds to overload the dilithium matrix. As the ship disintegrates, however, he transports himself onto Enterprise and attempts to kill Soong, but Archer manages to kill him first. Soong returns to the Starfleet Detention Center and learns that his previous work is being stored in a secure location for potential future use. He doubts that will ever happen, and begins to ponder perfecting artificial lifeforms instead.