Captain Jonathan Archer has just reached the primary junction in the central core of Cold Station 12. The captain has less than forty seconds to save everyone on board the station. He manages to isolate the control room, but unfortunately, the clock reaches zero, and the pathogens are released inside the ventilation grid. Dr. Jeremy Lucas informs Archer that he has less than a minute before he becomes contaminated.
Because Enterprise, situated nearby, is unable to obtain a transporter lock on Archer due to interference within the station, Archer orders Commander T’Pol to fire the starship‘s phase cannons at exterior hatch J-9 to decompress the station’s central core. As the pathogens almost reach Arche, Enterprise destroys the entrance to the shaft where he is located. The captain is then blown out of the station due to decompression, and as he clears the top of the central core into space, he is quickly beamed aboard Enterprise by Commander Tucker.
We are back in the stolen Klingon Bird-of-Prey, as it crosses into Klingon space. Doctor Arik Soong goes to the bridge and Malik very reluctantly gives up the captain’s chair. Soong asks about the Enterprise, and when he’s told that the ship is holding its position, he notes that “Archer’s not foolish enough to follow [them]” Malik responds that they won’t see Archer again, as he believes Archer is dead. This triggers an angry confrontation between Dr. Soong and Malik. Still in a state of anger and unsatisfied with the ship’s lack of speed, Soong attempts to reassert authority over Malik by ordering him to engineering to make some repairs to the engines, which Enterprise has previously damaged. Malik balks, saying he’s not an engineer, but then Soong tells him to go anyway, saying “You’re a bright boy, Malik, I’m sure you’ll figure it out.” Malik then leaves the bridge in a sulk.
Archer, T’Pol, Doctor Phlox, Lieutenant Malcolm Reed, and Commander Charles Tucker discuss plans to stop Soong and his Augments in Enterprise‘s sickbay. To better the odds in Enterprise‘s favor, the Starfleet officers decide to emulate a Klingon warp signature in order to slip past the Klingon patrols. T’Pol reports that the Dr. Lucas and his team are anticipating their return to Cold Station 12 to begin decontamination of the station. Commander Tucker notes “that’s quite a mess they gotta clean up.” T’Pol says that Lucas estimates it will take more than a year to fully decontaminate the facility.
On the Bird-of-Prey, Soong talks of taking the Augments to an area flooded with radiation from supernova remnants. Soong knows that there are signs of at least two habitable planets and it would be difficult to find them within the clouds of radiation. Malik is not happy about this plan. Soong tries to explain the need for a safe haven for the embryos to develop. Malik tries to reason with Soong, arguing that Starfleet won’t give up so easily. Soong asks Malik what he would do, but Malik is uncertain, only that running away is not the answer. Malik then asks if Soong is familiar with Botany Bay, a “pre-warp vessel launched at the end of the Great Wars.” Malik goes on to recount how the vessel left with many of “their brethren”, including their leader Khan Noonien Singh. Malik points out that Khan made the fatal mistake of running away from his enemies on Earth rather than facing them. Malik does not want to make that same mistake, he wants to face Starfleet rather than constantly running and hiding. Soong ends the argument by stating that “the matter is not open to debate.” He orders the ship to head to the Briar Patch.
As the Augments head towards the Briar Patch, Enterprise positions itself on the border to Klingon space. Commander Tucker reports that the warp coils have been realigned to look like a Klingon battle cruiser, but he warns the captain “this trick’s not gonna work if we get within 80,000 kilometers.” The captain puts the Enterprise on tactical alert and orders a course into Klingon territory at warp 4.
Meanwhile, back on the Bird-of-Prey, Malik enters Soong’s temporary laboratory. Soong asks Malik to stop challenging him in from of the others. Soong also asks Malik to trust that he knows what is best for the group. Soong begins to talk about how it wasn’t easy after he left, but Malik interrupts by asking about the embryos. Malik realizes Soong is manipulating the embryos’ DNA, to remove aggression and violent behaviour, and questions Soong’s right to do so, arguing that what Soong is trying to fix might be exactly how their creators wanted them to be. The discussion is interrupted by a call from the bridge.
On the bridge, Peris tells Soong that a ship is approaching at high warp. The ship is quickly identified as Enterprise. The earth vessel arms torpedoes and Captain Archer orders Soong to drop out of warp or face the consequences. Malik is in shock at the sight of Archer. The Augments shoot first with little effect; Enterprise returns fire, causing aft damage to the Bird-of-Prey. Malik wants to engage Enterprise, while Soong does not, noting Enterprise out-guns them “three-to-one.” In desperation, Soong orders that the Denobulan pilot be placed on board the shuttle. The Bird-of-Prey makes a detour to a star system with a gas giant, where Soong ejects the shuttle into the gas giant’s atmosphere, between two thermal layers. Enterprise, sees everything. Soong hails the Enterprise, telling Archer that the shuttle pilot is fine and will stay that way for “the four or five hours” it will take Archer to mount a rescue. Archer acknowledges the situation he’s in, allowing Soong to escape, though he warns the doctor that this isn’t over.
Soong and the Augments are working on repairs to the Bird-of-Prey. Malik has worked to cloak the warp trail so that Enterprise cannot follow them. Malik quickly tells Soong of the two dozen canisters of biogenic agents he beamed aboard the ship from Cold Station 12. Soong is immediately horrified by the act. Malik tells Soong the biogenic agents can be placed aboard a torpedo to create a bio-weapon, and fire it at a nearby Klingon colony named Qu’Vat. Malik quickly outlines how hitting the colony with the agents would kill every living thing. Malik’s reasoning is that once the Klingons learn it was Humans who decimated their colony, they would declare war on Earth and keep them “busy for years.” Soong immediately recognizes it as mass murder, but Malik will not be dissuaded. Soong tries to order Malik back to the bridge, but Malik no longer has any fear or respect for Soong.
The Enterprise rescues the Denobulan and turns to finding the augments’ ship through enhancing the sensors. T’Pol takes the opportunity to try to talk to Tucker, since it seemed like he had been avoiding her since her wedding. He admits as much, and says it will take time for him to adjust. He also says he was proud of her for what she did. He goes on saying they wouldn’t have made a good couple anyway. Just then, a beep alerts the two to a subspace distortion 0.4 light-years away, and Tucker calls Archer to say they may have found the ship.
On the Bird of Prey, in his quarters, Malik tells Persis that he is ready to take command away from Soong. Persis is reluctant to go along, but Malik tells Persis that while Soong may have raised them, “he’ll never be one of us.” Malik is angry that Soong will not go along with his plan to use the biogenic agents as a weapon against the Klingon. Malik tells Persis that Soong is altering the embryos’ genome, “making them weak and docile like ordinary Humans.” This is a change that Malik can’t abide. In the end Malik convinces Persis to go along with his plans of mutiny. Not long after, Malik, Persis, and two other Augments enter Soong’s lab and ask him to come with them. Soong wonders if Malik is going to kill him if he refuses. When Malik says that no one else has to die, Songs asks about the millions Malik plans to kill with his bioweapon. Malik doesn’t answer. Persis tells there is no other way, and when Soong looks at her in the eyes, she lowers her stare. Malik orders Persis to lock Soong in his quarters.
Enterprise is in Klingon space and is detected by another Klingon ship just 0.3 light-years away. With the universal translator updated to more dialects of Klingon and the ship 2 minutes away from exposing them, Archer decides to try to fake his way out. He pretends to have Chancellor M’Rek on board for a classified mission negotiating with the Orions. The Klingon wasn’t notified of this and asks why they don’t have the official transponder turned on. Archer responds they need to keep a low profile and demands the Klingon not mention this to his superiors. The Klingon appears to accept it and the ship moves off. Reed is very surprised that worked.
While confined to quarters, Persis visits Soong and explains why she went along with Malik, that he would have killed her if she hadn’t. Soong understands, then tells Persis that if Malik deploys the weapon he will confirm what Earth has always feared about the Augments, in the process destroying them all. Soong tries to plan some way to disable some key ship system, but in the end both Soong and Persis realize Soong needs to get off the Bird-of-Prey. Persis takes the internal systems off-line and helps Soong to leave in an escape pod.
The Enterprise eventually picks up the pod’s automated distress beacon, pulling the pod and Soong back aboard the Enterprise. He’s taken to the brig, where he finds it difficult to explain to Archer why he came back, and to try to get Archer to stop Malik and his plans. In the end Soong tells Archer about the three hundred kilograms of biotoxins that are missing from Cold Station 12’s inventory, and that Malik intends to use them on the Klingon colony. Soong goes on reminding Archer that he saw what Malik did on the station, that Archer knows what Malik is capable of.” Archer realizes that Soong didn’t know how the Augments were. Soong tries to tell Archer that if Soong had been there for them none of that would have happened, but Archer tells Soong that in the end “none of that would have mattered. It’s in their nature, they were engineered this way. Superior ability breeds superior ambition.“
Archer decides to believe Soong for the time being, and sets course to the Klingon colony. To get there on time, the ship has to travel at a high warp speed that might compromise the phony warp signature.
Back on the Bird-of-Prey Malik confronts Persis in private. He asks her who she thinks helped Soong escape, and she’s trying to put the blame on Lukesh. Malik dismisses every argument Persis has, and she ends up picking a knife to attack Malik. After a quick fight, Malik kills Persis with the knife.
As Soong works with T’Pol and Tucker, he apologizes to T’Pol for the business with the Orions. When Trip asks Soong to stay focused on what he’s doing, Soong notices that Tucker is a little protective of commander T’Pol. Trips say he just don’t like Soong very much. T’Pol detects a ship, a Klingon D5-class battle cruiser. Because of Enterprise‘s high warp, the ship has picked up Enterprise‘s warp signature and, listening to their hail, obviously recognizes them as an Earth vessel. They demand they prepare to be boarded.
Archer tries to warn the Klingon captain, Magh, but the Klingon suspects it’s a trick and that Enterprise is the real attacker. Soong address him in Klingonese, saying Archer and crew are honorable people. Magh dismisses it and ends the hail. Archer decides to power down weapons and, when the battle cruiser tries to board Enterprise, Archer, orders the Enterprise’s grappler to target the port nacelle of the Klingons. The Enterprise goes to full impulse and eventually tears open a piece of the nacelle, disabling the ship. They continue on to the colony.
Meanwhile, Malik’s scans of the colony reveal three population centers. Malik plans to detonate over the southern in order to maximize the number of casualties. Problems with the torpedoes guidance systems and the appearance of Enterprise on their long range sensors complicated Malik’s plans. On the Enterprise, intercepting the Bird-of-Prey turns to be problematic, as the engines are ready to blow up. The Augments are able to launch the bioweapon, but Enterprise manages to fire a trio of torpedoes, one of which manages to destroy the bioweapon.
The Bird-of-Prey shoots at the Enterprise, critically damaging most weapons. With only the aft cannon, Archer wants to target the bridge, but Soong helps him, and explains the bridge is protected, but the primary power grid is vulnerable. Archer trusts him and orders it, disabling the ship. T’Pol can only read 12 bio signs. Surprisingly, Malik prefers to die rather than be captured and proceeds to overload the dilithium matrix. Soong pleads with him to stop, but Malik argues it’s better to die there than be in prison. Soon, the Bird-of-Prey explodes.
Soong, stunned at the loss, is escorted in handcuffs to the crew quarters, for the trip back to Earth. Suddenly, Malik drops from the ceiling. Richards immediately fires, but that does not stun Malik, Malik then knocks Richards and Archer down, proceeding to kill Soong for betraying the Augments. As he holds him by the throat, Archer manages to kill Malik by blasting a hole in his stomach with Richard’s particle rifle.
Back on Earth, Soong is taken back to his very clean cell. Soong remarks “You’d at least let me finish my work before you take it away and destroy it.” Archer replies that none of his prior work during his time in prison has been destroyed, and is stored in a secure location for potential future use. Soong doubts that will ever happen. Soong, now believing that Humanity cannot be perfected, instead turns his attention to creating an artificial lifeform, though he doubts he’ll finish the work himself and that it might take a generation or two.“