Eleven years in the past, Arik Soong is giving a lecture about society's fear of genetically-engineered people to his Augment children. Malik asks if there is anyone else like them, and Soong says that there is, and one day it will be their duty to free them. In the present, Soong and the Augments take a Klingon bird of prey to Cold Station 12 to steal the Augment embryos. Malik wants to turn off the life support, but Soong vetoes it, since he doesn't want anyone killed.
The Enterprise, following the coordinates Soong gave them, goes to Trialas IV, where the Augments grew up. Trip finds that some medical equipment is missing, and Malcolm and the MACOs find Udar, who is the only person there. Udar tries to escape with a knife, but Archer knocks him unconscious.
On the bird of prey, Soong is looking at a PADD with information written by Raakin, a young astronomer. Noticing that none of the other Augments are willing to offer information, Soong asks Malik where Raakin is, and Malik claims that Raakin is dead. He reveals that not only is Raakin dead, but he killed him, though he claims it was self defense. Soong gets angry and punches Malik against the wall, but Malik apologises for the killing and Soong forgives him.
In sickbay, Archer talks to Udar, who, unlike his "siblings", has average intelligence and physical prowess. Udar refuses to tell Archer where the other Augments are, claiming that the Enterprise won't be able to stop them. Trip contacts Archer, telling him that the medical equipment that was stolen consisted of incubators. Admiral Forrest then contacts Archer, telling him that there are 1,800 embryos on Cold Station 12, that Soong is likely heading there, and to use whatever force is necessary to stop him. Meanwhile, the Augments hijack a Denobulan medical ship called the Barzai.
Archer goes to sickbay and learns that Udar can be discharged. He tells Phlox that Jeremy Lucas is the senior medical director of Cold Station 12. Phlox asks to join the boarding party, and Archer accepts. In the captain's mess, Archer tries to get some information out of Udar and tells him that he will be sent to school (surprising him, as he expected jail instead). When Udar calls Soong his father, Archer gives him a PADD with information on it, revealing that he had different biological parents. Meanwhile, the Augments knock everybody out with gas.
Archer meets Phlox in the mess hall, who is worried about Lucas, but Archer reassures him that they'll get to the station as fast as they can. Archer also brings up his father, who died of Clarke's Disease, perhaps wondering if genetic engineering should be legal after all.
The Augments break into Cold Station 12 and Lucas claims he no longer has access to the embryo chamber. Malik doesn't believe him, but Soong does, and has the team locked up. Lokesh begins working on cracking the access codes, then they detect the Enterprise. Soong hails Archer and forces him to turn the ship around, threatening to kill Lucas if he doesn't.
While Lokesh keeps trying to decrypt the codes (finding another layer of encryption), Malik finds proof that Lucas did indeed lie about not being able to access the embryo chamber. Soong orders Lucas out of the locked room and Malik suggests getting Lucas to fess up by shoving the deputy director into a tube and exposing him to a disease called "Symbalene blood burn". Soong initially is dubious, but Malik talks him into it, and the deputy director ends up dying while everyone else is forced to watch.
The Enterprise beams a team to the station before backing off, consisting of Archer, Phlox, Malcolm, Udar, and some MACOs. They (with effort) stun someone and Phlox leads them to the life support's controls. Meanwhile, Soong begs Lucas to give him the information, but Lucas refuses, so Soong tells Malik to release the anti-pathogen. Malik refuses, so Soong does it himself. By then, Lokesh has detected the anomaly caused by Archer's team and the MACOs have been captured. The Enterprise, realising that the team is captured, goes back to the station and hails it. When Soong answers, Archer tells T'Pol to have Hoshi activate the station's auto-destruct sequence.
Hoshi's transmission doesn't get through, so T'Pol tries using the weapons to attack the station, only for the Klingon ship to attack Enterprise from behind and fly away. Malik, realising that Phlox and Lucas are friends, exposes Phlox to a pathogen. Lucas finally reveals the code, allowing Soong and the Augments to steal the embryos and get away. Soong wants Udar to come too, but Udar decides to stay instead. Malik decides to take some pathogens for himself as "insurance".
Saul puts Archer into the locked room with his team and the station personnel, so Archer knocks him out with the door. Malik arrives, wanting to kill Archer, and the two fight. Feeling like he doesn't have the time, Malik sets the containment breach that will spread deadly pathogens all over the station, then kills Udar directly.
The Enterprise sees the shuttle leave for the bird-of-prey, but is too slow to disable the Barzai before it docks with the bird-of-prey, which then jumps to warp. Lucas tells Archer how to stop the breach; Archer then runs off to the station's primary junction, with just under four minutes to save everyone.
Tropes in this episode include:
- Bond Villain Stupidity: Malik thinks it's a good idea to tell Archer that he'll unleash every pathogen in the station after they leave, rather than just shoot him.
- Call-Back:
- Lucas (Phlox's friend and pen pal from "Dear Doctor" and "Doctor's Orders") makes his onscreen debut.
- Phlox had previously told Archer that his species hibernates for six days. In one scene, he mentions that he's approaching another sleep cycle.
- Combat Compliment: Malik calls Archer a "competent fighter" while beating the crap out of him.
- Curb-Stomp Battle: Not surprisingly, Archer is no match for Malik.
- Do Not Call Me "Paul": Udar prefers to be called by his nickname, Smike.
- False Flag Operation: Soong and the Augments capture a Denobulan ship and use it to infiltrate CS-12.
- Forced to Watch: Lucas, when one of his doctors is subjected to Symbalene blood burn. The threat of making him watch Phlox die the same way is what finally breaks him.
- Genre Blindness: Soong learns that the Augments lied about Udar being dead and actually banished him for being weak. Malik says it was Raakin's order, but they all went along with it. Soong is surprised by that despite the nasty history of Augments in general, and Archer calls him on it.Archer: Why are you so surprised? Whenever a group of people start believing they're better than everyone else, the results are always the same.
- I Didn't Mean to Kill Him: Malik tearfully says that killing Raakin was an accident. Soong buys it hook, line, and sinker.
- Instant Sedation: The sedative gas takes out everyone in the control room in seconds.
- I Will Punish Your Friend for Your Failure: When Lucas doesn't break despite getting punched in the face, Malik decides to go after his colleagues.Malik: Some men are braver with their own lives than they are with the lives of others.
- Mercy Kill: Rather than let Udar die of the pathogens that are about to be released all over the station, Malik simply shoots him.
- Narrative Profanity Filter: At one point, Lucas whispers something into Soong's ear. Soong responds with "That language is unbecoming for a man of science."
- Self-Destruct Mechanism: Archer orders T'Pol to remotely activate the one on CS-12. It fails, so they go with Plan B: destroy the station with torpedoes. That also fails.
- Sequential Symptom Syndrome: Soong describes what is happening to the poor doctor who's dying from Symbalene blood burn in graphic detail. Even he can't stand it.Soong: His temperature's rising quickly. Blood pressure's approaching critical. [...] Right about now, his extremities feel like they're on fire. But it's the capillaries, starting to burst.
- The Sociopath: If committing fratricide didn't already establish Malik as this, the Crocodile Tears as he recounts a false version of the incident should do the trick.
- Suddenly Shouting: Soong, when he can no longer stand watching the Red Shirt die of Symbalene blood burn.
- Super-Senses: While Udar isn't any stronger, smarter or longer-lived than the average human, he states that he still has the enhanced hearing of the other Augments, which is what he uses to try to alert Archer.
- Too Unhappy to Be Hungry: Phlox thinks he has to eat since he's lost weight recently and is preparing for hibernation, but can't bring himself to because he's too worried about Lucas.
- Torture Always Works: Zig-zagged. Soong, reluctantly, throws one of Dr. Lucas's colleagues into a booth and subjects him to a deadly disease in order to make him talk. However, Lucas refuses to give the access code and Soong cracks first, ordering the anti-pathogen to be released. However, Malik delays just long enough for it to be too late. Later, when Malik threatens to do it again to Phlox, Lucas gives him the code.
- Trojan Horse: The Augments capture a Denobulan medical shuttle and use its clearance codes to gain access to CS-12.
- Villain Has a Point: Both Archer and Phlox agree that Soong isn't so wrong for wanting to use genetic engineering to prevent diseases, like the one that killed Henry Archer.
- Your Mom:Lucas: You son of a bitch!
Soong: Actually, Mother was a chemist.
