A troop of superhumans invades a Klingon bird-of-prey, decimates the crew, and takes over their ship. With Klingons threatening retaliation, Captain Archer and his Enterprise crew are called upon to find the missing ship and bring the culprits back. Launching his mission takes him to an imprisoned brilliant scientist, Dr. Arik Soong. Soong "fathered" genetically-altered, strikingly attractive humans called "Augments," who possess remarkable strength, agility and intelligence. They're nearly indestructible, and are deemed responsible for the Klingon massacre.

Soong has been jailed for stealing the embryos that became Augments, raising them on a planet in the Trialas System until he was captured a decade ago. Soong claims that he has no idea why the Augments would have taken possession of a Klingon ship, but does convince Archer that he can make them surrender without a fight. Plus, Soong is familiar with the area the Augments are in — the Borderland — a volatile region between the Klingon Empire and the Orion Syndicate that is a magnet for danger. Despite the crew's skepticism, an electronically shackled Soong joins the mission.

As Enterprise enters the Borderland, Soong does seem initially helpful, particularly when the crew soon encounters trouble. During an attack by an Orion Interceptor, T'Pol and eight crew members are beamed from Enterprise into a teeming slave market. Held by hulking Orions, T'Pol and the other slaves are outfitted with restrictive neurolytic restraints — capable of causing painful convulsions — while they await being auctioned off. Desperate to get T'Pol and the others back, Archer enlists Soong's help in being admitted into the Orion Slave Market as the two seek out the kidnapped Enterprise members. Unfortunately, T'Pol has already been auctioned off to an Orion, but Archer succeeds in bidding high enough for all the other members of his crew. When the would-be slaves are beamed back to Enterprise, Trip analyzes a purloined neurolytic restraint so that he can send a code to Archer and Soong that would free T'Pol from her restraint.

As Archer and Soong then punch up the code that frees T'Pol, bedlam breaks loose in the slave market as others are unexpectedly freed as well. However, Soong takes this golden opportunity to make his own getaway, and he and Archer wage a battle against each other in the chaotic slave market. Fortunately, Archer prevails, but he realizes that Soong lured Enterprise into this Orion ordeal precisely to plan his own escape. After Archer and Soong are beamed back aboard Enterprise, Archer demands that Soong lead him to the Augments, but a jailed Soong refuses. He pities Archer for not understanding the potential and supremacy of his genetically engineered Augments.

Meanwhile, aboard the apprehended bird-of-prey, a power struggle has taken over the Augments as their number-two leader, Malik, seeks to emerge victorious over Raakin, the group's leader up until now. As they are all in complete and utter devotion to their missing "father" — Dr. Soong — Malik feels Raakin has been leading the Augments astray. However, Malik's lover Persis feigns her devotion for Raakin, helping Malik unleash his plan to dominate the group. As Malik succeeds in rallying the other Augments to follow his command, he and Persis lure Raakin into a trap where he is killed by Malik.

Shortly afterward — with Malik at the helm — the Augments' bird-of-prey damages and hails Enterprise, seeking to dock. Malik comes aboard, disgusted that their beloved Soong has been relegated to the brig. Nearly choking Archer to death while Reed and some MACOs stand by helpless, the overpowering Malik demands that Soong be released. When Soong is, he and the Augments are euphorically reunited. Soong then tells Malik to spare Archer and his crew; Soong and the Augments will be too far away from Archer and a damaged Enterprise to be found and caught. Then, on board the bird-of-prey with his Augments, Soong ominously announces that they are going to build a new world together and must now retrieve the thousands of Augment "brothers and sisters" waiting to be born.