Archer has approached the primary junction in the centre of Cold Station 12. He has forty seconds to divert the power to the secondary relays, so that he can seal off the lab and prevent many dangerous pathogens from infecting the people in there. He succeeds, but he's still in danger. Enterprise can't beam him up due to interference with the central core, so T'Pol gives the order to fire at a hatch to decompress the central core. They do so, and Archer is blown into space and instantly beamed aboard.
The Bird-of-Prey which the Augments stole crosses Klingon space. Soong enters, and Malik updates him, then asks him about the Enterprise, which Malik says is holding its position. Soong claims that Archer isn't "foolish enough" to follow them, but Malik thinks Archer is dead. This makes Soong very angry since he said not to kill anybody without his order, and when Malik tries to justify himself, Soong threatens to throw him into a "targ pit" for a month. He orders Malik to engineering to repair a piece of equipment which the Enterprise crew broke, but Malik is unsure since he isn't an engineer. Soong tells him that he's smart and will figure it out on his own.
Meanwhile, T'Pol has evacuated the away team from the station and removed all signs of infection from Archer. In sickbay, Archer, T'Pol, Phlox, Trip, and Malcolm discuss ways to stop the Augments. Malcolm notes that there are six Klingon patrols that will intercept Enterprise if it follows the stolen Bird-of-Prey, so the crew decides to sneak past by faking a Klingon warp signature. T'Pol reports that Dr. Lucas and his team are returning to Cold Station 12 to clean up the pathogens, which they estimate will take over a year.
On the Bird-of-Prey, Soong plans to take the Augments to an area flooded with supernova radiation, known as "Klach D'kel Brakt" to the Klingons and the "Briar Patch" to the humans. There are at least two habitable planets there, and the radiation would make them hard to find. Malik doesn't want to hide again, but Soong points out that they need to keep the embryos safe. Malik thinks that there's no point in hiding, since Starfleet won't give up until they find them. Soong asks Malik what he would do, but Malik doesn't know; he just points out that Khan also ran away and it ended badly. Soong decides to head for the Briar Patch anyway.
Enterprise prepares to enter Klingon space, with Trip having changed the warp coils to fool the Klingons. Meanwhile, on the Bird-of-Prey, Soong, in his impromptu lab, tells Malik to stop challenging his authority. Malik thinks that a "son" should be allowed to "disagree with his father", but Soong tells Malik that he has to trust his decisions, noting that he used to have faith in him. Malik claims that back then, he was just a naive kid. They begin talking about the embryos, only for Malik to get mad when Soong reveals that he's engineering them to remove any violence. This starts an argument between them because Malik sees it as needless tampering, but Soong sees it as ironing out the mistakes.
A ship approaches, which is revealed to be Enterprise, and Archer readies his torpedoes and orders Soong to drop out of warp or else. They fight for a bit, but Soong doesn't want to fight as the Enterprise is much more powerful than the Bird-of-Prey. He flies it near a gas giant and launches a shuttle piloted by a Denobulan into the atmosphere, saying that the shuttle pilot will be okay but only for the next four or five hours. Thus, Archer lets Soong escape, but tells him it isn't over.
The Enterprise goes to save the Denobulan, while Soong and the Augments do repair work. Malik reveals that he cloaked the warp signature and then tells Soong about the twenty-four canisters of biogenic agents he beamed from Cold Station 12. Soong is shocked and Malik tells him that he can use the biogenic agents to make a bio-weapon. Soong thinks Malik wants to fire it at the Enterprise, but he actually wants to fire it at a Klingon colony called Qu'Vat, thus causing a Klingon/human war. Soong points out that this is mass murder and tries to order Malik back to the bridge, but Malik won't budge.
The Enterprise succeeds in rescuing the Denobulan, then enhances the sensors and finds the Bird-of-Prey. T'Pol talks to Trip, noting that he's been avoiding her since she got married, and he replies that he's adjusting, but that he's proud of her and that due to their species, they'd have made a bad couple anyway. A machine then starts beeping, revealing a subspace disturbance that may be from the Bird-of-Prey.
In bed, Malik tells Persis that he wants to steal command from Soong. She isn't sure, but he says that Soong will "never be one of [them]" and is still angry about Soong's refusal to let him start a war and altering the embryos to make them "weak and docile". He eventually talks her into going along with the mutiny and they and two others lock Soong in his quarters.
A Klingon ship detects Enterprise and Archer tries to trick them by pretending to have Chancellor M'Rek on board for a negotiation with the Orions. The Klingons ask why he doesn't have the transponder on, but he claims he needs to keep a low profile, threatening to make the Klingons work on a garbage scow if they tell their superiors, to which the Klingons leave.
Persis explains to Soong why she went along with Malik: he would have killed her otherwise. Soong understands and says that if Malik deploys the weapons, it will confirm people's biases about Augments and kill a lot of people. He tries to think of a plan to disable a key ship system, but eventually both agree that he needs to get off the Bird-of-Prey, so she sends him off in an escape pod.
The Enterprise picks up the pod's distress beacon and brings it onboard with Soong in it. Archer puts Soong in the brig, where Soong tries to explain why he came back and get Archer to stop Malik. Soong claims that if he had been there when the Augments were teens, Malik wouldn't have gone bad, but Archer believes that "superior ability breeds superior ambition".
Archer decides to believe Soong, who helps them track down the Augments despite T'Pol's concerns that it's a trap. Meanwhile, Malik has found out that Persis helped Soong escape and attacks her, eventually killing her with a knife. T'Pol finds a Klingon battle cruiser, who recognises them as an Earth vessel due to the high speed interfering with the fake warp signature and having heard a hail from them. They, led by a captain named Magh, want to board the ship, believing the Enterprise crew to be malevolent even when Soong tells them in Klingon that they're not. They use the grappler to pull a bit of nacelle off the Klingon ship, disabling it, and then move on.
Malik scans the colony and finds three population centres. He decides to detonate over the southern hemisphere, since that's where two of them are. However, the torpedoes guidance systems wonk out and Enterprise shows up. Unfortunately, he manages to launch the bio-weapon due to problems in the Enterprise's engines, but thankfully, the Enterprise manages to destroy the weapon.
The Bird-of-Prey fires back and damages all of the Enterprise's weapons except the aft cannon. Archer wants to fire at the bridge, but Soong points out that the bridge is protected, while the power grid is vulnerable. He tries it, and it works, then Malik explodes the ship, preferring to die than be imprisoned.
Soong is put into crew quarters to be taken back to Earth. While Archer is explaining what will happen, Malik drops from the ceiling. Richards tries to stun him, but it doesn't work, so Archer kills him by blasting him in the stomach. Soong is taken to prison, where he's told that his work is in storage, but he's decided to give up genetic engineering and begins working on an artificial lifeform instead.
Tropes in this episode include:
- Artistic License – Geography: Trip mentions that his parents have moved from Panama City, Florida to Mississippi. This implies that their old home was destroyed in the Xindi attack. However, Panama City is located in the Florida panhandle. The probe's weapon strikes near Lake Okeechobee, which is in the far south of the state.
- Attack Its Weak Point: Soong points out a vulnerable spot on the Bird-of-Prey for Enterprise to target.
- Bittersweet Ending: All the Augments die, and Soong is deeply saddened by their loss. As he's returned to prison, he mentions to Archer that he's going to refocus on cybernetics. The episode ends with him grabbing his paper and pencil, beginning work on an artificial lifeform that he estimates will take a generation or two to finish.
- Call-Forward:
- Malik brings up the SS Botany Bay and its complement of Augments, including Khan Noonien Singh. Soong dismisses the ship as a myth.
- Soong wants to take the Augments to one of the inhabited planets in a nebula he calls "the Briar Patch."
- Soong also mentions that the area is referred to by the Klingons as "Klach D'kel Brakt," which was the site of a major battle between the Klingons and Romulans referenced in "Blood Oath."
- Soong decides to start the groundwork on an artificial lifeform. His grandson will complete his vision with Data.
- Chekhov's Gun: We'll be seeing Qu'Vat colony again before the season is out.
- Deadpan Snarker: Soong's reaction to a hail from Archer after Malik said that he was dead from the pathogens."He sounds pretty confident for a dead man."
- Dramatic Irony: Soong decides to establish a new colony with the Augments on one of the planets in the Briar Patch. The Ba'ku would have already settled in the area by this point.
- False Flag Operation:
- Trip modifies Enterprise's warp signature to look like a Klingon ship.
- Malik plans to do this by destroying a Klingon colony, which will then be blamed on the humans.
- Heel–Face Turn: Persis is the only one who does not side with Malik, and is killed for it.
- Istanbul (Not Constantinople): It turns out that the Briar Patch and Klach D'kel Brakt are the same nebula. Soong says that his choice of name is catchier.
- It Only Works Once: Archer manages to bluff a Klingon patrol. Later, as a result of pushing the engines too fast, they're detected before he has a chance to do this again.
- Living Lie Detector: Malik deduces that Persis helped Soong escape because only four people know the codes for the internal sensors and they were the only two not on the bridge. He then notes that Persis's heart is beating faster, which gives her away.
- The Mutiny: After chafing against Soong's authority, Malik finally seizes control.
- Mythology Gag: The shot of Malik activating the self-destruct is framed in almost the same way as Khan activating the Genesis Device.
- Not Quite Dead: Malik is presumed dead after he self-destructs the Bird-Of-Prey, but he really slipped onto the Enterprise to murder Soong for his betrayal. Archer, a mere human mind you, shoots him dead just before he does.
- Pop-Cultural Osmosis Failure: One of the Augments doesn't recognize the name "Briar Patch." Soong replies that he should have read more of the books he left.
- Refuge in Audacity: Archer tells the Klingons that Chancellor M'Rek is on his ship. It actually works.
- Sadistic Choice: To get the Enterprise off his and the Augments' backs, Soong has the Denobulan pilot from the previous episode bundled into a shuttle and launched into the atmosphere of a gas giant. Her craft is left caught between two thermal layers, giving her about four or five hours to live — long enough for Enterprise to rescue her, but they can't do that and chase the Bird-of-Prey at the same time.
- Self-Destruct Mechanism: With the Bird-of-Prey critically damaged, Malik overloads the dilithium matrix.
- Shoot the Bullet: Enterprise destroys the Klingon torpedo with one of her own.
- Thrown Out the Airlock: After isolating the control room from the pathogens, Archer has himself spaced to avoid being infected. Because Space Is Cold, Enterprise beams him up half-frozen.
- Torso with a View: Archer uses a rifle to shoot a small hole straight through Malik.
- Would Hit a Girl: Malik kills Persis with a knife.
