With 47 minutes to a potential reactor breach on Enterprise NX-01, Archer forms a plan which involves transfering Trip from Columbia to Enterprise … while traveling at warp 5. He reaches to Malcom, who has experience with the procedure, although at a much lower speed. T’Pol is working on calculations to merge the warp fields of both starships, but the vessels will have to be less than fifty meters apart. Archer says that Travis can handle the flying, so long as Malcolm can bring Trip safely aboard. Malcolm muses that Archer will have to let him out of the brig.
Trip gets ready to go, as Columbia turns on it back and comes under Enterprise. With the Columbia nearing final position and their warp fields contacting, the two ships shake momentarily. T’Pol heads to engineering to prepare everything for Trip. Malcolm fires the tether across, and Trip begins his trip over. However, as T’Pol detects a fluctuation in the warp field, and Travis begins to have trouble maintaining a good distance from Columbia. Trip asks what is happening, but Malcolm tells him he’s doing fine, before realizing that he has to hurry up. T’Pol is unsuccessful in diverting enough power to the warp field, and Trip is released from the tether just before it snaps.
Trip can think of only one way to fix the warp engines: a cold start. Shutting down the engine will reset the algorithms, and when it restarts, the subroutines will be back to normal. Enterprise will have to enter Columbia’s warp field during the procedure, so that Enterprise’s engine doesn’t explode. They will only have a minute or two, though.
Heading for engineering, Trip notes the two MACOs outside the launch bay. Malcolm says he has had a slight misunderstanding with the captain, and heads back to the brig, much to Trip’s confusion.
Gathering stats on the engines, Trip notes that someone “hasn’t taken very good care of [them]”. T’Pol suggests he “speak(s) with the Klingons”. Trip announces he will perform a manual shutdown and restart in two minutes, leaving T’Pol very perplex.
Trip is showing off !!
Hernandez contacts Enterprise, and informs them that they’ve routed everything they can to the warp field. Archer gives Trip the go-ahead and the engineer performs the shutdown procedure. As soon as the nacelles power down, Trip sets the engineering crew to work. Hernandez tells them they have about 40 seconds. With mere seconds to go, the warp engines spark into life and the extended warp field collapses, but Enterprise is warp-capable again. Trip asks that Enterprise drops to impulse, so he can look things over. Archer asks Hernandez and Columbia to stick around for a while.
Back on Qu’Vat Colony, Doctor Antaak finds Phlox in his cell, who has been brutally handled by the general and his men. Phlox asks Antaak to contact Starfleet, as he refuses to create Klingon Augments. Antaak however has been looking over Phlox’ research, and has found a weakness in the virus. Phlox notes that he’s right, but K’Vagh wouldn’t get his Augments, and would therefore never allow it. Antaak thinks they should do it without telling the general, who will eventually find out, but Antaak notes that saving millions of innocent lives would give them both a more honourable death.
Malcolm is taken, rather forcefully, to his quarters where Archer is waiting for him. On his screen is a picture of Harris. Archer has used the database to identify Harris, who worked in Starfleet Security up to five years before. Malcolm says there is nothing more to add, but Archer finds that unacceptable, as Malcolm has put every member of the crew at risk. Saying he is only following orders, Archer retorts that he’ll go to Starfleet and blow open the whole conspiracy if he has to. As Malcolm doesn’t know anything else, Archer tells him to contact Harris, so he can find out himself.
Antaak and Phlox are comparing family histories, and Antaak sees that Denobulan mating practices must be “very complex”. Phlox asks the Klingon about his family, and the older man replies that his own father disowned him when he became a healer. He then blames himself for the Augment virus, and Phlox is there ultimately because of his failure.
The Bird-of-Prey with the Klingon Augments arrives back at the colony, and Laneth reports that the Enterprise was destroyed. K’Vagh sees that one of them is missing: his son. Laneth says that he was killed by the Humans, and it was therefore without honour.
K’Vagh checks up on the two doctors, who report excellent progress. Phlox claims to have found the “switch” that will “turn off” the virus; he will have it within the hour. K’Vagh contacts Krell, and learns that his project has been shut down by the Klingon High Council. He argues that all their research will be lost if the colony is sterilized. Krell says that the colony will be spared if K’Vagh is successfully within three days, the time it will take the fleet to reach Qu’Vat.
On Enterprise, Trip says he’ll help out the vessel’s new chief engineer, Kelby. He then asks why Malcolm is in the brig, but Archer says he can’t go into it for the moment. Trip decides to head back to Columbia, and T’Pol offers to walk him down. On the way in a corridor, T’Pol asks him if Trip is having any problems, specifically with sleep but he says that he’s fine. He asks if she is sleeping well and she awkwardly replies that she is and then promptly leaves him.
K’Vagh returns to the lab and tells Phlox they are running out of time. The Denobulan asks how K’Vagh’s son contracted the virus. The Klingon reveals that they tested the virus on prisoners first, and when they had none left, Command chose a unit to be experimented on – the unit in which his son belonged. His son asked for no special treatment, and K’Vagh gave him none.
Malcolm is tucking into his small dinner in the brig, but Marab, the Klingon next door to him, refuses to eat his meal, objecting that is it dead. Malcolm questions the Klingon need to fight, but he replies that anyone questioning that need would be imprisoned, if not killed. As Malcolm notes that that’s not the way things are done in Starfleet, Marab believes that this is why the Klingon Empire will defeat the humans. Malcolm however, notes that the Klingon is sharing the same brig as he is.
Laneth and her shipmates are all becoming weak as a result of the virus, and that they’ll stay together, as comrades, until they die. K’Vagh tells them that Phlox is working on stabilizing the effects, and they will all be healthy again. Laneth wonders if their appearances will stay the same, as she thinks otherwise they will be outcasts on their own world. She also tells the general that she felt fear for the first time, in the battle with Enterprise, and thinks they are all becoming weak like the Humans. K’Vagh assures them that he will not let the Empire turn their back on them as long as he is alive.
Archer is sitting in his quarters with Porthos. His line of thought is broken as Harris contacts him, telling him that Phlox is on a mission of great importance to Starfleet. Archer objects that starfleet would never allow the kidnapping of one of its personnel, but Harris directs Archer to Article 14, Section 31 of the Starfleet Charter. Harris states that Malcom has done some good work for them over the years. Archer informs Harris that Malcolm was put into an impossible situation, but Harris replies there’s more to it than just one captain and one ship. If Phlox is stopped from completing his mission, the repercussions will affect entire worlds.
Phlox holds four strains, one of which has the genetic trigger to stop the virus before it becomes lethal; unfortunately, he doesn’t know which one. He will need a week to check, but as Krell won’t extend his deadline, Phlox must infect four healthy Klingons. K’Vagh, Antaak and two guards are in the room, so the general advises Phlox to infect them instead.
In Archer’s ready room, Malcolm is explaining to the captain why he joined Section 31 as a young ensign. He hasn’t done any other work for them since before joining Enterprise. Archer shows him the medical scans of Marab, and thinks that it is a military experiment that went wrong. Harris also claimed that a cure needed to be found in order to create a more stable Empire for Starfleet to deal with. Malcolm confesses that he wanted to tell Archer everything, so the captain tells him to decide where his loyalties lie. Although Malcolm doesn’t know where Phlox was taken, Starfleet Intelligence knows that there is a genetic research facility on Qu’Vat Colony, and that is a good place to start.
Archer reinstates Malcolm, who returns to the bridge much to the surprise of the bridge crew. Enterprise is six hours from Qu’Vat Colony, and Malcolm recommends that Columbia withdraws to a safer distance so that Klingon patrols don’t have a single target.
Phlox asks K’Vagh why he chose to pursue the Augment project, when Soong failed. The general replies that Soong’s only mistake was making only a few Augments, and that Klingons have discipline – although Phlox points out that Augments don’t. Preparing the final strain, Phlox injects K’Vagh with it, and the general asks if bloodwine would affect the results. As Phlox replies that he doesn’t believe so, the Klingons begin to drink. K’Vagh offers him some but Phlox refuses, saying he never drinks while on the job.
Archer is interrogating Marab in sickbay, who is becoming ill like his shipmates. Remaining defiant, Archer tells him that if he won’t help them, he can at least help his own people. Marab agrees.
Phlox is taking scans of Laneth, who has become very ill, when Antaak enters, saying that the guards are displaying the first symptoms of the virus. Phlox also scans Antaak, but the look on his face tells all: K’Vagh has the cure, and Antaak will die. Phlox assures Antaak that if they work quickly enough, he too can be cured.
Krell is enjoying a bowl of gagh when Harris contacts him, saying that the Klingon failed to stop Enterprise or Columbia. Krell asks Harris to order both ships to withdraw, but Harris has no authority to do that. Krell says he will have to destroy them. Harris reminds Krell of the arrangement and that it would benefit both Starfleet and the Empire, but Krell laughs it off, saying that Harris believed him.
As Antaak prepares to extract the cure from K’Vagh, Archer enters the room, phase-pistol at the ready. Marab enters behind him, to the astonished K’Vagh. Archer announces his intentions to retrieve Phlox, to which K’Vagh insists that the Klingons need him – at which point the doctor cuts both of them of. He asks Archer for a few more hours to cure the virus. K’Vagh is furious that he will cure the virus rather than perfect the Augment genome as he’d promised, but with the captain there to back him up, Phlox informs the general that he was lying.
Malcolm’s sensors pick up the three Klingon warships in orbit, but communications to Columbia are jammed. On the surface, an alarm makes the Klingons aware the ships have arrived, and Archer has no luck contacting Enterprise. Krell informs that the colony will be eradicated, against Archer’s objections, claiming he has a “more effective solution”. Phlox speaks directly to Krell, transmitting details of the anti-virus, but Krell says his orders are clear, claiming both Enterprise and Columbia as property of the Klingon Empire.
Krell gives his tactical officer orders to proceed, and to leave nothing standing. His battle cruiser enters a lower orbit and begins to fire on the colony. Enterprise attempts to disable the enemy ship’s disruptors, but is constantly drawn away by the two birds-of-prey. The Columbia arrives on scene, taking up a position behind the birds-of-prey, attempting to distract them while Enterprise disables the battle cruiser. Phlox says he will be able to finish creating the cure faster if he has a Human host to replicate enough antibodies. Archer notices he is the only Human there, and knows the risks. Sitting down on the chair in the middle of the lab, Phlox straps him in.
Columbia disables the engines on one of the Klingon ships as their shields begin to fail. Phlox informs Archer of the possible side effects he will get from being injected with the virus. On Enterprise, Oshi manages to cut through the jamming signal, but as Archer isn’t available, Phlox talks to them instead, asking them to protect the colony until his work is complete. T’Pol orders Travis to place the ship directly between the battle cruiser and the colony, and orders Malcolm to increase power to the hull plating. In the lab, K’Vagh looks on as ridges appear on Archer’s forehead.
The Klingon battle cruiser attempts to throw off Enterprise by shifting orbit, but the Starfleet ship stays with them. Finally breaking through the interference, T’Pol asks Hernandez for help, only to find that Columbia has lost its weapons. At Qu’Vat, Archer breaks free from his restraints, so K’Vagh holds him down while Phlox extracts the antibodies. During the process, Antaak has prepared a canister containing the virus, and sends it to Krell’s ship, infecting its crew.
Phlox speaks to Krell, telling him the contents of the canister, but Krell believes he’s lying. Phlox tells him to either check his internal sensors or wait half an hour. Krell brands it a cowardly attack, but Phlox says that if the cure is destroyed now, he too will die from the virus, unless he orders his ships to stand down. Reluctantly, Krell agrees.
Antaak is in Enterprise’s sickbay, having been treated successfully. He complains that his targ won’t be able to recognize him now that he has a smooth forehead, which he calls a disfigurement. Phlox tells him he did his best to correct all his mistakes, which is all he could ask of himself. As he realizes his superiors will most likely end his career as a geneticist, he will have to find a new specialty – maybe in cranial reconstruction, something Phlox believes will soon become very popular. As Phlox goes to check on the captain, Antaak stops him for a moment, and thanks him for all that he did.
Archer is recovering, although he feels like having some gagh. Phlox says that his cranial ridges, along with his cravings for Klingon cuisine, will disappear within a few days, but Trip says he should keep them – as he looks intimidating. Trip says he will be staying around for a little while longer which, T’Pol muses, will make Kelby “delighted”. Trip reminds her it will only be temporary.
Malcolm is in his quarters, quietly reading, when Harris contacts him, thanking him for his work. As the conversation progresses, Malcolm tells Harris never to contact him again, but Harris tells him that recruitment policy dictates that no one can just walk away. Malcolm’s reply is simple, he answers to one man alone: Jonathan Archer. Cutting Harris off mid-sentence, Malcolm returns to his reading.