A Klingon scientist works in a laboratory, watched by a Klingon general and a guard. A Klingon prisoner is led into the laboratory by two Klingon soldiers. In Klingonese, the prisoner claims that his death sentence was commuted and demands to speak with the magistrate who presided over his trial. He is strapped to a chair and a vial of green liquid is hung above his head, which the scientist injects him with. The prisoner cries out as his cranial ridges ripple and begin to dissolve.

Act One

Returning to Earth, Enterprise finds the NX-class starship Columbia in the orbital drydock facility, undergoing final preparations for her maiden voyage.

Meanwhile, Commander Tucker is packing a technical manual for Enterprise into a bag. He looks through a window as the construction work to Columbia is being completed. When T’Pol enters his quarters, Trip remarks that the new starship is a thing of beauty. T’Pol states that Enterprise and Columbia are virtually identical, although Trip claims that an experienced engineer can see the differences. Tucker asks if T’Pol is goig to his “going away party”. She says she doesn’t see the logic behind the his departure, he says he will find serving aboard Columbia more challenging. He believes he can fine tune Columbia in half the time it took him to do for Enterprise. T’Pol asks if he’s leaving becuase of her, to which he states that not everything in his life revolves around her. She leaves.

In San Francisco, Phlox and Hoshi are just leaving “Madame Chang’s“. Phlox is surprised that it was so busy there, but it turns out that Hoshi had told a few of her Starfleet friends about the restaurant. Phlox is considering a job offer from the Interspecies Medical Exchange to serve as their Director of Xenobiology, although he says he would find it difficult to leave his Enterprise shipmates.

Suddenly, two shadowy figures step out of an alleyway and order Phlox to accompany them. When asks what they want, one of the figures aims a disruptor at the Phlox’s head. Hoshi busts some Aikido against them, but a third figure appears behind her and knocks her to the ground. Phlox is struggling with one of the figures when a disruptor blast hits him, rendering him unconscious. He is restrained and carried away as Hoshi lies on the ground, barely conscious. As her eyes flutter, she hears one of the men say something in an alien language.

Archer and Malcolm arrive at the scene, and they meet up with Commander Collins of Starfleet Security. Hoshi tells them that she is fine. Collins recalls that the Hoshi had told her the figures had spoken in a foreign, or alien, language. Collins tells Archer and Malcolm that the only DNA which they could find belonged to Hoshi and Phlox, although they had also detected some ionization traces nearby. Malcolm suggested that it might have been a transporter signature, although isn’t convinced. Collins wonders whether this might be a grudge revenge from a few months ago when Phlox had an altercation with a human xenophobe, but Malcolm doesn’t think that the human in question would be capable to find his head with both hands, let alone coordinate a kidnapping. Collins informs Archer that Starfleet Security will continue to thoroughly investigate the crime and leaves. Archer asks Malcolm to check whether Starfleet Operations satellites picked up any transporter activity nearby.

Aboard Columbia, Tucker informs the engineering staff that they will have to align the dilithium matrix to within 0.3 microns. When Ensign Rivers replies it should be 0.5 microns, Tucker answers that he probably has more practical experience than the warp field specialist who wrote the technical manual. He orders Biggs and Pierce to recalibrate the warp field stabilizers and asks Rivers and Strong to start work on the injector assembly.

As the engineers begin their duties, Tucker notices that Captain Erika Hernandez has entered engineering. The captain reminds him that it is Starfleet protocol for a transferred officer to report to the captain when they come on board and asks Trip to come to the captain’s mess for a meal later the next day. Before she leaves, Hernandez advises him to report to the quartermaster and update his uniform patch.

In the captain’s ready room aboard Enterprise, T’Pol enters and informs Archer that Phlox’s wives have been notified of his kidnapping. Archer tells her that although Hoshi was barely conscious, she thought she heard Phlox’s kidnappers say something in an alien language. Archer asks T’Pol to conduct a mind meld with Hoshi. When the Vulcan worries that she has never initiated a meld before, Archer replies that he will advise her with the knowledge he gained from carrying Surak‘s katra.

Meanwhile, in Enterprise‘s armory, Lieutenant Reed is puzzled when he discovers that Starfleet satellite grid 137 was off-line for maintenance at the time that Phlox was kidnapped. When he contacts Starfleet Operations, there is no reply. A Human male dressed in dark clothing appears on the viewscreen which Reed was using to check the satellites. The man, Harris, claims he will tell Reed why the satellite grid was down if the lieutenant meets him at a specific address in San Francisco.

In a darkened room, T’Pol tries to meld with Sato. When the ensign senses the meld isn’t working, Archer suggests that the Vulcan tries to slightly relax her emotional suppression. Eventually, their minds merge. T’Pol helps Sato remember a time just before she and Phlox were assaulted. The Vulcan appears in Sato’s mind and the ensign indicates to the shadowy figures before they attack. When they begin their assault, Sato struggles to focus. The ensign manages to focus long enough, however, to remember the men’s words. She realizes that the aliens spoke in the Rigelian language.

On the bridge, T’Pol reports to the captain that a Rigelian freighter left Earth approximately two hours after Phlox was captured. The freighter was scheduled to travel to Proxima colony, although the vessel’s trajectory would suggest it was heading elsewhere. Canceling shore leave for the crew on Earth, he exits the bridge to contact Admiral Gardner in his ready room.

At night in a foggy San Francisco, Reed meets up Harris, whom he soon discovers was involved in shutting down the satellite grid. When Reed asks him if he knows Phlox’s location, Harris answers that the section he is working for requires Reed’s help. The lieutenant implies that he used to be employed by the same section, although he believed his tenure to be over. Harris claims that if Reed doesn’t provide the assistance which is required, Phlox may die.

Act Two

In the same laboratory where experiments were conducted earlier, the Klingon general, K’Vagh, watches the scientist prepare another vial of green liquid to be tested. Restrained by two Klingon soldiers, Phlox is led into the lab. K’Vagh welcomes the Denobulan to the Qu’Vat Colony and warns him he will die unless he cooperates with Doctor Antaak, the Klingon scientist. When Phlox assumes he will be assisting Antaak, the general corrects him that he will be in charge. Antaak recognizes Phlox from an IME Conference on Tiburon in 2149. When Phlox fails to recall Antaak, the scientist claims he was disguised as a member of the Mazarite delegation because Klingon medics weren’t invited to the meeting. As K’Vagh leaves, he states that he expects Phlox to prepare a progress report by sunrise on the following day. Antaak apologizes for the general’s impolite behavior, a characteristic of the warrior caste. The scientist reveals that the Klingons are facing their greatest threat since the Hur’q attacked the Empire – an infection which has claimed millions already. Antaak fears the Klingons may become extinct if the infection isn’t stopped. Phlox wonders why the Klingons didn’t just ask Starfleet for help, and Antaak replies that would have made the Klingons look weak and dishonorable. The scientist recalls how Phlox’s paper on viral propagation impressed him and tells the Denobulan he is interested in metagenic research. Antaak encourages Phlox to begin mapping the virus’s nucleotides, and repeats that the virus is a great threat to the Klingon people – while he didn’t like resorting to abduction any more than Phlox, it has occurred, and the need for his medical skill is very real.

On the bridge of Enterprise, T’Pol reports that she is no longer detecting the Rigelian freighter’s warp trail. Reed suggests that the freighter could have resumed its course on impulse power and Travis Mayweather mentions that Enterprise will intercept the vessel in 8.2 hours. When Archer hails engineering, no-one responds. The captain eventually speaks to his new chief engineer Commander Kelby and tells the engineer that Enterprise needs more acceleration. Kelby says he’ll try to increase the starship’s velocity.

On board Columbia, Trip Tucker and Captain Hernandez are enjoying a meal. Tucker remarks that the food tastes good, and Hernandez recalls that when she left her last assignment, Republic, she stole Captain Jenningschef. Tucker laughs, although his expression turns serious again when the captain makes him aware of two crew transfer requests since his transfer to Columbia. Not willing to reveal any names, Hernandez adds that she denied them their requested transfers, stating that engineering is already short-handed as it is. She comments on the impression Trip seems to have made with the engineering staff. Tucker doesn’t care about his impression as much as he does about his staff’s work. He notifies the captain that Columbia is almost ready for warp trials. Hernandez remembers that in an interview she saw with Tucker after Enterprise returned from the Xindi mission, the commander said he couldn’t imagine serving on any other vessel. She wonders what changed his mind. Trip explains the crew of Enterprise were becoming too familiar and that he sometimes prefers working with colleagues rather than friends.

In T’Pol’s quarters, the Vulcan is meditating. In her mind, she and Tucker are in a completely white place. She asks him why he is with her, as he isn’t usually in her meditations. Tucker replies that the same question puzzles him and T’Pol explains that they are in her meditation. Tucker comments that he doesn’t find the white place as interesting as a beach or the Fire Plains she showed him on Vulcan. When T’Pol asks Tucker to leave her meditation, the engineer retorts that she should leave and reveals that the white space is his daydream. Rivers disturbs Tucker’s reverie and the commander returns to the real world. Rivers hands him a diagnostic on a PADD and walks away.

In her quarters, T’Pol is puzzled by her meditation. Archer contacts her from the bridge and informs her that Enterprise is nearing the coordinates of the Rigelian freighter. Rising to her feet, the Vulcan tells Archer that she is heading to the bridge.

Later, the bridge’s viewscreen displays the wreckage of the Rigelian craft. T’Pol determines that all of the vessel’s Rigelian complement are dead and that there are no Denobulans on board. When Archer questions Reed if he can identify the vessel’s destroyer, the lieutenant checks the sensors which state that the weapon signatures are have been successfully identified. However, Reed erases the alert from his screen and lies to the captain that he can’t verify an identification. Believing the lieutenant’s deception, Archer orders him to scan for the ship’s data recorder.

On Qu’Vat Colony, Phlox believes that the Klingon virus is a mutated form of the Levodian flu. Antaak remarks that the virus is highly immune. Phlox suggests contacting the IME, who may have experience of dealing with the virus. The Denobulan adds that no-one at the IME would have to know specific details. However, Antaak sees no reason for the IME to become involved, as the Klingons stole their entire medical database. Phlox and Antaak discuss the morals of stealing medical research. Soon, General K’Vagh returns with another prisoner and a guard. Phlox examines the prisoner and concludes that the Klingon has been infected. The Denobulan worries that he and the uninfected Klingons are being exposed to the virus but Antaak reassures him that the infection only becomes contagious at stage three – the prisoner is currently only at stage one.

When Antaak draws a weapon and aims it at the prisoner, Phlox stops him before he fires it. The Klingon scientist and Denobulan doctor argue about the ethics of euthanasia. Suddenly, K’Vagh removes a disruptor from his belt and kills the patient himself, leaving Antaak and Phlox shocked.

In his quarters, Reed opens a secure channel to Harris. The lieutenant communicates his frustration that the section of Starfleet which Harris works for destroyed the Rigelian freighter. When Reed asks what the complement of the Rigelian ship was, Harris refuses to reply. Reed discloses that he has completed an analysis of the weapons signatures and that he hasn’t told Archer the identity of the destroyer vessel yet, although he doesn’t know how long he’ll be able to keep that information secret. Harris implies that Reed could say Orion raiders destroyed the Rigelian vessel since they operate in the area but the lieutenant suggests divulging his secret to Captain Archer. Harris reminds Reed of Archer’s duty as a captain and advises the lieutenant to become comfortable with Harris’ orders. He recalls that Reed agreed to serve Harris’ section long before he was assigned to Enterprise. As an explosion rocks the ship, Hoshi hails the crew and orders the crew to man the battle stations. Shortly before Reed closes the channel to Harris, he explains that Enterprise is under attack.

Act Three

As a Klingon ship fires its disruptor cannons at Enterprise, Reed falls out of a turbolift onto the bridge. T’Pol announces that the Starfleet ship’s hull plating is holding, although the Klingons are not responding to Ensign Sato’s hails. Archer orders Reed, now at his post, to target the warship’s weapons.

Meanwhile, a Klingon boarding party transports into a corridor on Enterprise and shoots an officer who tried to call for help. Unlike usual Klingons, the members of the away team are missing their cranial ridges. They race through the corridor and enter an access tube.

On the bridge, Sato confirms the presence of the intruders. Archer instructs Reed to seal the access tube where the Klingons are and deploy a team of MACOs.

When one of the Klingon attackers races to a computer panel, another Klingon, Marab, issues the officer an instruction in Klingonese. The MACOs arrive and fire phase rifles at the Klingons. Marab shoots back but the MACOs hide from view and none are injured by the Klingon’s disruptor fire. Using a communicator to contact his ship, Marab orders the warship to target the MACOs’ location.

In space, Enterprise fires its phase cannons at the Klingon craft. However, the warship thrashes the Starfleet vessel, pounding the starship with its disruptor cannons as it swoops downward before it slowly recedes.

On board Enterprise, Marab watches as the section where the MACOs are located explodes, forcing them to retreat.

On the bridge, Archer authorizes Reed to disable the Klingon ship to prevent it from escaping.

Meanwhile, the Enterprise computer terminal that a member of the invading boarding party is working on displays Klingon text and graphics, which the Klingon soon disguises and returns to Starfleet characters. Satisfied that their work is completed, the Klingons head to the area of the ship where they beamed aboard. On the way there, however, Marab is shot by a MACO and lands beside a bulkhead. Another of the Klingons fires back and the MACO is thrown to Enterprise‘s deck by his disruptor blast. The boarding party is forced to flee when they become aware of armed security officers running towards the, leaving Marab behind.

On the bridge, T’Pol and Travis detect that the boarding party has transported aboard the warship, which has activated its warp drive. At Archer’s command, Travis attempts to pursue the Klingons but the helm station doesn’t respond.

When Archer later enters sickbay and questions Marab, the captain, T’Pol and Hoshi Sato are surprised to discover that their prisoner is Klingon, as Marab is missing the cranial ridges which are a usual feature of his species.

Later, Archer, T’Pol, Sato, Mayweather and Reed gather on the bridge. Reed theorizes that Marab may have been surgically altered to appear Human. T’Pol states that because the boarding party disabled Enterprise‘s antimatter flow regulators, the starship’s warp drive should take six hours to be repaired. The captain orders Travis to help Chief Engineer Kelby in analyzing the extent of the Klingons’ damage. As Reed listens, T’Pol informs Archer that the data which was stored in the Rigelian freighter’s data recorder has been erased. T’Pol complies with the captain’s request to work with Sato in an attempt to reconstruct the data.

On Qu’Vat Colony, Boshar – Antaak’s pet targ – nibbles at Phlox’s clothes. Antaak shouts at the animal to return to its domain. The Denobulan doctor is appalled when he finds Augment DNA in the mutagenic virus. General K’Vagh explains that the Klingon Empire could not allow the Human Augments, two of whom boarded and commandeered a Bird-of-Prey, to provide Starfleet with a superior advantage. Phlox argues that the Augments who were genetically engineered by Arik Soong were relics from a time from decades ago before Starfleet banned genetic engineering. K’Vagh tells Phlox that the Vulcans weren’t very persuasive when they told the same story to the Klingon High Council. When Phlox remembers that all of the Augments which Soong created were killed, he wonders where the Klingons obtained the Augment DNA. Antaak replies that several embryos were found on board the Bird-of-Prey which the Klingons used to resequence the DNA of some test subjects. However, the subjects exhibited several unexpected side effects – their cranial ridges began to dissolve and they were more aggressive than the other Klingons had anticipated. For a time, it seemed that the experiments had been successful. The Klingon Augments were stronger and more intelligent, though they later suffered an excruciating death when their neural pathways began to degrade. One of the test subjects was suffering from the Levodian flu, which was modified by the Augment genes to become airborne. When Phlox becomes irritated that he wasn’t given this information earlier, K’Vagh orders him to return to his work.

Aboard Enterprise in the situation room, T’Pol suggests to Sato that using a recursive algorithm may help to reconstruct the directory of the Rigelian data recorder. When Sato asks T’Pol about the side effects of a mind meld, the Vulcan replies that the procedure entails the sharing of subconscious thought. These thoughts can sometimes surface during sleep, causing strange dreams. Sato continues by admitting that she recently had a bizarre dream – one in which Trip was involved. As T’Pol listens intently, she learns that Sato’s dream shared a certain parallel with the meditation she experienced earlier – Trip was in a strange, white place.

Sato reveals that although she has never dreamed about Commander Tucker before, her dream had a romantic quality to it. T’Pol hears a console signal, returning her attention to the computer’s analysis of the data recorder.

Later, Archer, T’Pol and Sato are in the captain’s ready room. Archer holds a microdyne coupler which was used to erase the data recorder’s memory core. The coupler was found in storage locker C-14, which was last accessed by Malcolm Reed.

Archer later calls Reed to the captain’s ready room. There, the lieutenant hears the evidence against him. Reed acts as if he is innocent and insists that the Rigelian freighter was attacked with Orion weapons. Archer contends that T’Pol examined Reed’s analysis and concluded that Klingon disruptors destroyed the freighter. When Archer asks for an explanation, the lieutenant refuses to answer. The captain opens the door of his ready room, where a MACO corporal, W. Woods, stands. Relieving Reed of his duties, Archer orders the MACO to escort the lieutenant to the brig and confine him there.

Act Four

In Enterprise‘s brig, Archer informs Reed that the starship is heading into Klingon territory, a dangerous place to go. The captain asks Reed if he knows where Phlox is, but the lieutenant assures Archer that he doesn’t. Archer seems appalled and surprised that Reed would commit treason, although the armory officer insists that he isn’t working for the Klingons. When the captain asks who did recruit Reed, the lieutenant doesn’t answer. He implies that he has an obligation to withhold certain information and is disgraced by the thought of his father, Stuart Reed, learning that Malcolm is facing court martial.

On Qu’Vat Colony, General K’Vagh has become impatient with Phlox. The doctor notes that Arik Soong would have been able to map the virus more efficiently than the Denobulan. Antaak states that the Klingons tried to abduct Soong but he was under heavy guard. K’Vagh reveals that the Klingon High Council has launched a fleet of ships which have annihilated N’Vak Colony, one of the first planets to be infected. Phlox is appalled that the victims of the plague are being massacred, although K’Vagh argues that the Council are absolutely determined to contain the outbreak. When the Denobulan notifies K’Vagh that the development and testing of an antiviral agent will take weeks, the general worries that millions of Klingons will have been infected by that time. He tells Antaak that the fleet will reach Qu’Vat Colony in five days, although the scientist claims that the Council wouldn’t order the colony‘s destruction if they learned that Klingon Augments had been created there. Although the experiments haven’t been successful yet, Antaak informs K’Vagh that he and Phlox may be able to sustain the Augments’ DNA. If successful, K’Vagh could then use the Augments to force the High Council into allowing more time for the research of a cure. When Phlox refuses to cooperate in the creation of the Augments, K’Vagh pulls a disruptor from his belt and orders a Klingon soldier to take the Denobulan away.

On Columbia‘s bridge, Captain Hernandez contacts the dockmaster, who permits the starship to depart. She then hails Engineering, where Trip is ensuring that final preparations are complete. Ensign Rivers reports that the dilithium matrix is stable and the drive coils are properly configured. Trip notifies the captain that engineering is ready, so Hernandez gives the order to engage aft thrusters as Columbia departs spacedock, before going to warp.

In space, the new starship launches from the orbital dry dock station, before plunging into the depths of space at warp speed.

Aboard Enterprise, a partition within the brig’s cell has been added, dividing it into two. Reed watches as a couple of MACOs enter and push Marab into one of the cells. As the MACOs exit, the lieutenant speaks with Marab, who thinks Reed is fortunate to be alive after lying to the captain. He reveals that if a Klingon betrayed their captain, he would be immediately executed. Reed claims that his goal is the same as Marab’s – a cure. Suddenly, the starship shudders.

On the bridge, Travis reports a malfunction in the matter/antimatter intermix chamber. The pressure of the warp plasma is increasing and the anti-matter flow regulators are locked open. T’Pol is unable to determine whether the Klingons damaged the regulators. Travis states that the pressure of the warp plasma is approaching critical levels. If Enterprise dropped to impulse velocity, the warp reactor would breach. However, if the starship’s speed increases, the pressure of the warp plasma would fall. Archer instructs Travis to go to maximum warp and orders T’Pol to assist the engineering crew.

In the brig, the captain demands Marab to instruct Archer how to repair the damage which the Klingons did. When the captain explains that Marab will die if Enterprise‘s reactor breaches, the Klingon states that he is prepared to die. When Reed shouts that he can help, Archer leaves the brig, not listening to the lieutenant’s pleas.

In Main Engineering, T’Pol and Kelby learn that the warp matrix has been compromised by a Klingon subroutine, which has also infiltrated the command protocols. Although T’Pol is uncertain whether she will able to remove the subroutine, she states that she will try her best to help regain control of the ship.

In a turbolift, Archer is contacted by Travis, who tells the captain the warp plasma pressure is rising again. The captain orders Travis to increase Enterprise‘s velocity to warp 5.2, a speed which the starship won’t be able to hold for long. Eventually, the ensign complies and the starship races through space to an uncertain fate.