The Augments (episode)
Dr. Soong's Augments acquire additional Augment embryos as well as biological weapons from Cold Station 12. A desperate plan is devised to use the biological weapons to foment a war between the Klingons and Earth in an attempt to flee Earth's control forever.(Part 3 of 3)

Summary

Teaser
Captain Jonathan Archer has just reached the primary junction in the central core of Cold Station 12. The captain has forty seconds to divert the power to the secondary relays in order to isolate the central lab and keep "hundreds" of lethal pathogens from reaching the lab personnel as well as the  away team inside the lab. Unfortunately, the captain can't completely stop the pathogens from being released; as the clock reaches zero, he's informed by Dr. Jeremy Lucas that the ventilation grid will carry the pathogens throughout the rest of the station, including the central core. At that point he has less than a minute before he becomes contaminated.

Act One

Because Enterprise, situated nearby, is unable to obtain a transporter lock on Archer due to interference within the central core, 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 begin to be released, Enterprise destroys the top of the shaft where Archer is located. The captain is blown out of the central core due to decompression. As he clears the top of the central core into space, Archer is quickly beamed back aboard Enterprise by Commander Tucker.

The augments' stolen  just crosses into Klingon space. Doctor Arik Soong goes to the bridge and Malik informs him. With a glare, resulting from the conflict between them, he takes the captain's chair and asks about the Enterprise. Malik informs him that the ship is holding its position. Soong notes that "Archer's not foolish enough to follow us." Malik responds that they won't see Archer again, as Malik believes Archer is dead. This triggers an angry confrontation between Dr. Soong and Malik. Dr. Soong becomes furious, shouting "No one was to be killed without my express order!" When Malik tries to excuse his actions, Soong interrupts and tells Malik that if Malik disobeys him again that he'll lock Malik in the Bird-of-Prey's targ pit where Malik "won't see the light of day for a month." 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 repair the port inducer assembly, which Enterprise damaged previously. Malik balks, saying he's not an engineer. Soong tells Malik to go back anyway; "You're a bright boy, Malik, I'm sure you'll figure it out." Malik then leaves the bridge in a sulk.

Meanwhile, still in temporary command of Enterprise, T'Pol records a log entry.

"First officer's log, supplemental. We've evacuated the away team and all personnel from the station. The captain shows no sign of infection. He's recovering in sickbay."

Archer, T'Pol, Doctor Phlox, Lieutenant Malcolm Reed, and Commander Charles Tucker discuss plans to stop Soong and his Augments in Enterprises sickbay. Reed notes there are a half dozen Klingon patrols that will intercept Enterprise if it follows the Augments' stolen Bird-of-Prey into Klingon space. To better the odds in Enterprises 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 remnant. He refers to it by its Klingon name of "Klach D'kel Brakt", or more colloquially as the "Briar Patch". 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 impatiently interrupts Soong with "This is your plan? To hide, again." Soong tries to explain the need for a safe haven for the embryos to develop. Malik tries to reason with Soong that Starfleet won't give up, that they'll send other ships to pursue them, that the "gas cloud" won't protect them. 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. Soong states that the Botany Bay is a myth and that there is no evidence it ever existed. Malik believes that it does, but his point is 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 but instead 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 Commander Tucker 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 tells Malik "you have to stop challenging my authority in front of the others." Malik responds with "Can't a son disagree with his father? I thought we were family." Soong tells Malik he's willing to overlook what he's done up to that point, but that Malik has to trust that Soong knows what is best for the group. Soong says "You used to have faith in me!", and Malik replies "I was a child then, I didn't know any better." 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 behavior. Malik says "You're changing its personality.", to which Soong replies "I'm correcting a defect in its genome." Soong goes on to tell Malik that genetic engineering was in its infancy when he was conceived, and that they weren't able to correct "all the mistakes." Malik takes exception to that analysis. He says "What right do you have to tamper with their genome?" Soong replies "Trust me… I know what I'm doing!" Malik retors "You don't know that this is a defect. Maybe this is the way our creators wanted us to be." The discussion is interrupted by a signal from the bridge: a ship is approaching at high warp.

The ship is quickly identified as Enterprise. Soong orders an increase in speed as Enterprise arms torpedoes and Captain Archer orders Soong to drop out of warp or face the consequences. Malik is in shock as Soong remarks Archer "sounds pretty confident for a dead man." 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, following, 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.

Act Two 

While the Enterprise works to rescue the Denobulan, 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 easily reacquire their position. 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 Soong assumes Malik means to fire it at Enterprise. Malik quickly fills Soong in on his idea to 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. Malik says "What happened to you in prison? You're not the man who raised us. The man who was willing to do whatever was necessary."

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 marriage. 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 also says they wouldn't have made a good couple anyway – Vulcan and Human. 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.

Later, in his quarters, Malik tells Persis in bed 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 Malik's play to use the biogenic agents as a weapon to launch the Klingons and the Humans at each others throats, protecting the Augments from both. 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 Malik's plans of mutiny. Not long after, Malik, Persis, and two other Augments take Soong prisoner in his lab and lock him in his quarters.

Enterprise is in Klingon space and is detected by another Klingon ship (with a Klingon crew this time) 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, threatening garbage scow duty. 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; Malik 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.

Act Three 
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 Soong soon 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. Archer already knew about the loss. Soong tells Archer about Malik: "You saw what he did on the station; you know what he's capable of." Archer replies "You didn't know. You had to see him murder someone in front of you." 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… superior ability breeds superior ambition. One of their creators wrote that. He was murdered by an Augment."

Archer decides to believe Soong for the time being, and Soong is soon helping the Enterprise crew to track the Augments in their Bird-of-Prey. T'Pol is concerned that Soong is leading them into a trap, but Archer believes Soong. To get the to colony, 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, determining that Soong escaped with Persis' help. In the end Malik and Persis have a fight, and Malik kills Persis with a d'k tahg knife.

As Soong works with T'Pol and Tucker, T'Pol detects a ship, a Klingon  battle cruiser. Because of Enterprises high warp, the ship has picked up Enterprises warp signature and, listening to their hail, obviously recognizes them as an Earth vessel. They demand they prepare to be boarded.

Act Four 
Archer tries to warn the Klingon captain, Magh, but he 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 ship tries to board Enterprise, Archer, orders the ship's grappler to target its port nacelle. 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, two in the southern hemisphere and one in the northern. 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. Problems with Enterprises engines make an intercept with the Bird-of-Prey over the target colony problematic. The ship is 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 fires back, 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. 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 crew quarters this time for the trip back to Earth. As Archer tells him he will speak for him on his behalf, Malik drops from the ceiling. Richards immediately fires, but it does not stun him, Malik knocks him down and Archer, 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 myself. Might take a generation or two."

Memorable quotes
"Come on. It's not like we would have made an ideal couple. A Vulcan and a Human? Romeo and Juliet probably stood a better chance."
 - Tucker, to T'Pol

"Is there something we can do to keep from showing up on their sensors?"
"I could paint a bird of prey on the hull."
 - Archer and Tucker

"I wasn't aware the doctor discharged you."
"He didn't. What's our status?"
 - T'Pol and Archer

"How long can we sustain warp five?"
"As long as the captain wants it. Or until we blow up, whichever comes first."
 - Soong and Tucker

"Are you familiar with the name Botany Bay?"
"It's a penal colony on the shores of Australia."
"It's also the name of a pre-warp vessel launched at the end of the great wars. The ship carried many of our brethren, including Khan Noonien Singh."
"Botany Bay is a myth! There's no evidence it ever existed."
"All records of the launch were destroyed. They didn't want to be followed."
"Even if you're right, the ship was lost, never to be heard from again."
"That's exactly my point. Khan was a great leader, but he made one fatal mistake. He ran from his enemies rather than face them."
 - Malik, Persis and Arik Soong

"You could at least let me finish my work before you take it away and destroy it…"
"No one's destroyed anything. It's being stored in a secure location – maybe someday, we'll figure out how to use it to benefit Humanity."
"I wouldn't count on it."
 - Soong and Archer

"I've been thinking – perfecting Humanity… may not be possible. Cybernetics… artificial lifeforms… I doubt I'll finish the work myself… might take a generation or two…"
 - Soong, back in his cell, thinking towards the future

Background information

 This is the last time Paul Sklar plays MACO R. Richards, Jermaine Soto will reprise the role in .
 This episode concludes the "Augment" story arc.
 The scene of a gravely-injured Malik crawling through the ruined bridge is slightly familiar and possibly a homage to a very similar scene with Khan in .
 The Briar Patch from  is mentioned here by Arik Soong as a place of refuge for his Augment children. Both Brent Spiner (Soong) and director LeVar Burton had starred in Star Trek: Insurrection. Soong also claims that the Klingon name for the Briar Patch is Klach D'kel Brakt, which was mentioned by Kor in  as the site of a great victory by the Klingons over the Romulans.
 LeVar Burton had not directed an episode of Star Trek featuring Brent Spiner since  in .
 This three-part story arc established that in the 22nd century, genetic engineering was completely banned on Earth after the Eugenics Wars, even for genetic research which could be used to cure critical illnesses. At the end of the story, Archer expresses his hope to Dr. Soong that research into genetic engineering that could cure life-threatening diseases would actually be resumed. According to Dr. Bashir in , by the 24th century genetic engineering was indeed used by that time to treat serious medical conditions, though trying to genetically engineer Humans with "superior" abilities was still banned.
 At the end of this episode, Arik Soong claims "I've been thinking, perfecting Humanity may not be possible. Cybernetics. Artificial lifeforms. I doubt I'll finish the work myself; might take a generation or two." This is a direct link to the Soong family's work in upcoming centuries, culminating in the creation of the androids B-4, Lore, Data, and Juliana Tainer by his great-grandson Noonian Soong.
 The characters Khan Noonien Singh and Noonian Soong were both named by Gene Roddenberry for a friend of his, "Kim Noonien Singh," with whom he lost touch after World War II. By linking the characters via Arik Soong, the Enterprise writing staff retroactively provides a possible in-universe inspiration for the later Soong's first name (although the implications of the descendant of an infamous criminal being named after an even more infamous despot are unexplored).
 This episode was heavily edited by Channel 4 when they broadcast it in the UK, removing the whole of the fight between Malik and Persis and its conclusion. As a result, Persis simply disappears from the episode without explanation.
 John Billingsley called the episodes making up the Augments arc some of the best work of the season. 
 The talk about the Botany Bay and Khan foreshadows the events of .
 This episode's ending on a positive note suggests that Soong may eventually be released from prison. At this point, it wasn't clear if he had fathered any (biological) children yet as no existing family was mentioned.

Continuity 
 The universal translator does not translate the Klingon word Qapla' when the Klingon patrol ends the transmission with Enterprise.

Links and references

Guest Stars 
 Alec Newman as Malik
 Abby Brammell as Persis
 Richard Riehle as Jeremy Lucas
 Mark Rolston as Magh

Special Guest Star 
 Brent Spiner as Soong

Co-Stars 
 Adam Grimes as Lokesh
 Kristen Ariza as Augment #1
 Dayna Devon as N.D. Engineer
 J.D. Hall as Klingon Com Voice

Uncredited Co-Stars 
 Geneviere Anderson as operations ensign
 Jef Ayres
 Macarena Bianchi
 Fernando Chien as Saul
 Shawn Crowder as B. Cotton
 Yuri Elvin as 
 Evan English
 Henry Farnam as command crewman
 Scott Hill as Hutchison
 John Jurgens
 Ricky Lomax as W. Woods
 Tom Miller as Human doctor
 Paul Sklar as R. Richards
 Unknown performers as 
 Human doctor

Stunt doubles 
 Vince Deadrick, Jr. as stunt double for Scott Bakula
 Christopher Leps as stunt double for Alec Newman
 Angela Meryl as stunt double for Kristen Ariza
 Brian J. Williams as stunt double for Brent Spiner
 Boni Yanagisawa as stunt double for Abby Brammell

References
ability; ambition; artificial lifeform; Australia; automated beacon; away team; base pair; ; biogenic agent; bio-sign; biotoxin; bioweapon; bird-of-prey; Botany Bay; ; brain; Briar Patch; camouflage; central core; circuit; coil assembly; Cold Station 12; containment breach; critical malfunction; cybernetics; ; decompression; decontamination; Denobulan; Denobulan shuttle; dialect; dilithium matrix; directional array; dispersive armor; DNA; docking port; dozen; embryo; engineer; environment; escape pod; Eugenics Wars; evidence; exterior hatch J-9; flight path; garbage scow; gas cloud; generation; genome; grappler; Great Wars; guidance protocol; heart; hemisphere; high warp; hostage; hull plating; incubation; inducer assembly; intercept course; interference; kilometer; Klach D'kel Brakt; ; Klingon; ; Klingon chancellor; Klingon High Council; Klingonese; Klingon space; leader; long range sensor; long range sensor analysis; lovers' quarrel; low orbit; M'Rek; Magh's battle cruiser; main plasma junction; mass murder; medic; megahertz; Mississippi; murder; myth; neurotransmitter; Orion; Orion slave girl; overload; Panama City; pathogen; patrol; penal colony; phase cannons; plasma junction; population center; power grid; power surge; pre-warp vessel; primary junction; propulsion system; proximity scan; pylon; Qo'noS; Qu'Vat Colony; radiation; radiation hazard; relay; rescue mission; Romeo and Juliet; secondary relay; security code; sensor grid; shearing force; shuttlebay doors; ; subspace distortion; supernova remnant; tactical alert; targ pit; thermal layer; torpedo launcher; transponder; transporter lock; ; universal translator; upper atmosphere; ventilation grid; vessel scan; voltage; Vulcan; Vulcan (planet); warhead; warp coil; warp field; warp signature; warp trail; weapons bay; xeno-biology; Xindi incident

External links 
 
 
 

cs:The Augments
de:Die Augments
es:The Augments
fr:The Augments (épisode)
it:I potenziati (episodio)
ja:ENT:野望の果て
nl:The Augments
Augments, The