We’re on a Klingon Bird-of-Prey, as the crew discovers a transport shuttle containing two Human bio-signs. They use a tractor beam to get hold of the ship and send a team to get the two humans. While they are being escorted to the brig, they attack and murder the entire crew.
Back on Earth, Dr. Arik Soong sits in his prison cell. Jonathan Archer comes to visit him, he has some questions. After Soong reveals he his working on plans for improvements of the Human genome, Archer tells Soong about the Bird-of-Prey. According to Archer, it was attacked by Augments whose DNA matched ones that Soong stole from a medical facility when they were embryos twenty years before.
On the Enterprise, Captain Archer and his senior staff have a meeting, It is revealed that Dr Soong took the embryos on a distant planet and raised the children as his own. They have been left alone since they were 10, when Soong was captured 10 years ago. Nobody knows why they attacked the Bird of Prey, but Soong has offered to negotiate with the Augments so they’d surrender without a fight. Finding the Augments is the only way to avert a war with the Klingons.
On the Bird-of-Prey, a power struggle ensues when the Augment leader Raakin scolds Malik for stealing the vessel. Malik takes great offence to this action and contemplates Raakin’s future as their leader.
Soong is removed from prison and gets on board the Enterprise. He is introduced to T’Pol and Malcolm Reed, and then asks to meet Phlox in sickbay, so he could analyse the DNA that the Klingon recovered.
Trip and T’Pol briefly talk about the wedding but are interrupted by Captain Archer entering the bridge. As the Enterprise prepares to launch, Archer takes a moment to regard his reassembled crew and tells them he wouldn’t have it any other way, as the ship leaves space dock and warps towards the Borderland.
While the Enterprise travels at warp speed, Archer informs T’Pol that a Klingon ship was spotted, probably doing reconnaissance. T’Pol says her government is trying to work out a diplomatic solution. Captain Archer offers T’Pol a compass as a present for her first day of duty.
The enterprise crossed into the Borderland. In sickbay, Phlox and Soong have a discussion about genetic engineering and the Augments, as well as the disastrous Eugenics Wars of the 20th century. Phlox says his people have used genetic engineering to help cure disease for over two centuries, but that is very different from what Soong does. He is not pleased about Soong’s work and behaviour.
The Enterprise is attacked by two Orion’s interceptors. They transport nine people including T’Pol. Archer asks Soong how he can get them back. Soong replies they are probably on Verex III, being processed to be sold as slaves. Soong offers to guide Archer to this planet, as he used to acquire supplies from the Orions while on the run.
On the Bird-of-Prey, Malik and Persis, a female Augment, discuss the fact that Raakin is taking them somewhere far away to live their peaceful lives. He says this isn’t what their “father” would have wanted, to run away and hide. Malik suggests Persis could try to convince Raakin to reconsider.
On Verex III, T’Pol is fitted with some kind of device on her neck. She’s then thrown in a cage where she finds Ensign Jeffrey Pierce. He is obviously scared and T’Pol tries to make him calm down.
Arriving at Verex III, the Enterprise is able to enter the auction due to an old identification code used by Soong. He is fitted with a transponder so he won’t be able to escape without being tracked, then Archer and Soong beam down.
T’Pol is taken to the auction stand, and she is found to be a high demand individual and is sold for a high price to a Tellarite.
Archer is able to locate most of his crew in cells. Soong explains that the devices on thir necks are neurolytic restraints, so Enterprise is not able to beam them out. After Soong and Archer view an Orion slave girl up for auction, they find T’Pol but are interrupted by a guard.
On the Klingon Bird-of-Prey in the captain’s quarters, Persis tells Raakin of Malik’s upcoming plan to overthrow him and take his place as leader. She tells Raakin that Malik believes he is weak and is making all of the Augments weak. Persis further tells Raakin that Malik believes that if their “father” were with them he would choose Malik to lead them. Raakin announces that he will betray their father’s principles – by killing Malik.
Ensign Pierce is up next for auction. Archer buys him using his scanner and bribes an Orion to deactivate his restraint but to leave it on Pierce’s neck. Back in orbit of Verex III, Phlox removes the implant from his neck, so Trip can analyse it.
In a corridor on the Bird-of-Prey, Raakin attempts to kill Malik but, unfortunately for him, all of the Augments on the Klingon vessel have turned on him, choosing Malik as their new leader. This eventually leads to Raakin’s death at Malik’s hands and command of the ship is officially handed to Malik.
Trip finds a code to deactivate all the restraints, and Archer returns to the auction, along with Soong. Archer is able to deactivate all restraints for the slaves and a riot ensues. The Enterprise crew is beamed back to the ship, but Soong stuns the captain and escapes. He deactivates his transponder so he can’t be tracked. Archer climbs one of the slave cages and spots Soong, then activates his arm restraints. Soong uses this to climb a wall, but Archer catches up with him and deactivates the restraints, causing Soong to fall back to the ground. They return to Enterprise.
Archer accuses Soong, now locked in Enterprise’s brig, of having planned the whole thing, knowing the Orions would attack the ship. He says two of the captured crew may suffer permanent injury. Soong pleads with Archer to just leave the Augments alone ; they are the future of mankind. They’re stronger, faster, and live longer than the average Human. Archer tells him they are dangerous and have to be stopped and proceeds to leave. Soong tries to insist that genetic engineering could have saved Archer’s father, who was suffering from Clarke’s Disease ; those who had banned genetic engineering had condemned him to death. Yet the captain refuses to listen.
Tucker and T’Pol speak briefly in sickbay. He asks how her honeymoon was, and she says that although she was on Vulcan for two weeks after Tucker left, she spent the time in meditation, alone. Tucker says it isn’t really his business anyway.
Resuming their search for the Bird-of-Prey, the Enterprise is, again, attacked by two Orion Interceptors claiming they stole Orion property. Enterprise is suffering damage until a Bird-of-Prey appears and chases off the Interceptors. Docking with Enterprise, they find out it is the Augments.
Malik meets with Archer and tells him that Soong has contacted him and they have come to rescue him. Archer says his orders are to take the Augments back to Earth. Malik says Earth despises the whole idea of his kind, and besides they are superior to Humans. He warns Archer that he is going to attack him, then a moment later, he grabs Archer’s neck threatening to kill him if Malcolm or anybody else interferes. As the rest of the Augments break into the Enterprise, Malik, with Archer as a hostage, exits the ready room onto the bridge and then to the turbolift.
They proceed to the brig and release Soong. Persis hugs him and Soong smiles. At the docking port, Malik arrives with Archer in front of the rest of the Augments and Soong. Soong says he is proud of all of them, and tells Archer to go home and start learning to speak Klingon. Malik leaves Archer and returns to the Bird-of-Prey with the others. The ship warps out with the Enterprise unable to pursue due to damaged engines.
On the Bird-of-Prey, Soong takes command and tells the Augments that they are going to retrieve thousands of their “brothers and sisters” who are waiting to be born. “Let’s go get them”, Soong states to his “children”.