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 pathogen s 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 cannon s 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 . Archer , T ' Pol , Doctor Phlox , Lieutenant Malcolm Reed , and Commander Charles Tucker discuss plans to stop Soong and his Augments in " Enterprise " s 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 " Enterprise " s favor , the Starfleet officer s 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 . 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 coil s 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 kilometer s . " " 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 torpedo es 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 , 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 ) . With the universal translator updated to more dialects of Klingon , 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 Orion s . 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 " 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 . 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 sensor s complicated Malik ' s plans . Problems with " Enterprise " s 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 , saying 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 . " " " " Is there something we can do to keep from showing up on their sensors ? " " " " I could paint a bird of prey on the hull . " " " " I wasn ' t aware the doctor discharged you . " " " " He didn ' t . What ' s our status ? " " " " How long can we sustain warp five ? " " " " As long as the captain wants it . Or until we blow up , whichever comes first . " " " " 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 . " " " " 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 . " " " " 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 . . . " " Links and references . References . Australia ; biogenic agent ; Botany Bay ; ; Briar Patch ; coil assembly ; Cold Station 12 ; cybernetics ; ; Denobulan ; Denobulan shuttle ; dialect ; dilithium matrix ; dispersive armor ; engineer ; escape pod ; Eugenics Wars ; garbage scow ; genome ; grappler ; Great Wars ; hemisphere ; kilometer ; " Klach D ' kel Brakt " ; ; Klingon ; Klingon battle cruiser ; ; Klingon chancellor ; Klingon High Council ; Klingonese ; Qo ' noS ; Magh ' s battle cruiser ; M ' Rek ; megahertz ; lovers ' quarrel ; Mississippi ; Orion ; Orion slave girl ; Panama City ; penal colony ; phase cannon s ; Qu ' Vat Colony ; " Romeo and Juliet " ; shearing force ; ; tactical alert ; targ pit ; transponder ; ; universal translator ; Vulcan ; Vulcan ( planet ) ; warp coil ; warp signature ; weapons bay ; Xindi incident