In a corridor on the Orpheus mining facility on Luna, Earth‘s moon, two men that we will later know as Paxton and Mercer, confer on the health of a baby girl, Although she was sick, the monitoring equipment says she now getter better. The two men leave the room, leaving a Vulcan–Human hybrid baby girl alone in her crib.
Meanwhile, on Earth, the Enterprise crew has been called home to appear at a meeting of Human and alien delegates discussing the formation of a “Coalition of Planets“. Everyone applauds after a speech by Nathan Samuels, presiding over the convention – everyone except Trip, whom Jonathan Archer orders to clap louder than he currently is. While Phlox remarks that he enjoyed Samuels’ speech, the rest of the crew is dismayed by Samuels’ failure to mention their contributions, without which the meeting would not be taking place. As the meeting adjourns and the crew begins to leave, Samuels compliments Hoshi on the recent improvements she made to the universal translator. Travis is intercepted by Gannet Brooks, a reporter covering the event – an old flame who still expresses romantic interest. Across the room, T’Pol confides to Archer that Tucker had a point – the Enterprise crew was responsible for making the event possible – just before a woman approaches and gives her a vial containing a hair follicle. The woman warns “they’re going to kill her“, then collapses, fatally wounded from a phase-pistol shot to the abdomen.
Archer, Tucker, T’Pol, and Malcolm Reed join Phlox in the Enterprise sickbay a while later. The woman didn’t survive her wonds, and T’Pol reveals that her name was Susan Khouri, and she was a medical technician. An extensive DNA testing of the hair follicle by Phlox reveals that the hybrid child is Tucker and T’Pol’s offspring.
Shortly after, T’Pol is meditating in her quarters when Tucker arrives to discuss the matter. T’Pol assures him she was never pregnant, yet somehow knows the child is theirs.
Archer meets with Samuels elsewhere on the ship; Samuels refuses to let the news of the child out into public, afraid it will stir anti-alien sentiments which have been heightened since the Xindi attack against Earth, and hurt the newly formed coalition. Samuels urges Archer to let Starfleet conduct the legal investigation.
At Archer’s request, Reed meets in San Francisco at night with Harris, the shadowy Section 31 agent, for information. Harris notes that Reed had asked him not to ever contact him again but Reed says he contacted him. Harris tells Reed that by agreeing to see him, Reed is acknowledging he still works for Section 31. According to Harris, Khouri was a member of Terra Prime, an underground isolationist movement. Section 31 is planing Terra Prime is preparing something, and that it has to do with the child. If the crew can find the child, they’ll find the answers to the mystery of its origin, and what Terra Prime is up to.
In Paxton’s office on the Moon, Paxton and Mercer discuss Khouri’s – and Mercer’s – allegiances where the child is concerned. Mercer is conflicted over Paxton’s plans for the baby, but denies it. Paxton calls the child “an abomination” and claims “when the time comes, it will be treated as such”. Paxton sends for Daniel Greaves after Mercer departs and tells him to put together “a group” and to meet him at the “third junction in one hour”.
On Earth, Archer pays Samuels a visit in the delegates’ conference hall, where the Coridan ambassador argues with the Earth statesman. The Tellarites have been pushing for a trade embargo against the Orions, who have supposedly been attacking Tellarite freighters. As Archer joins them, Samuels introduces him to the ambassador, who excuses himself to go discuss diplomatic affairs with his government. The Starfleet chief investigator has rejected Archer’s request for a case file; Archer asks Samuels to intervene. After Samuels initially refuses, Archer reveals that he has learned Samuels was once a member of Terra Prime himself, which Samuels calls a mistake of his youth, having blamed a Denobulan pilot for his father’s death in a flight accident. Samuels realizes he underestimated Archer and agrees to get him the case file.
Brooks comes to see Mayweather in his quarters; she claims she’s doing a story on Enterprise from the crew’s perspective. They get into an argument over their past romantic relationship, but Mayweather agrees to give her a tour of the ship.
In sickbay, Tucker asks Phlox about the baby. The doctor reveals that it’s a girl. He also says there is no reason an half human half vulcan baby would not be perfectly healthy. Tucker discusses about his doubts over whether T’Pol is telling the truth, which Phlox dismisses as foolish. Tucker says his father always wanted a granddaughter, which he bugged Tucker’s sister about constantly. Phlox points out that he got his wish.
In his lunar complex office, Paxton watches a video recording of Colonel Phillip Green, made three years after a cease-fire ended World War III. Greaves enters; they discuss the moral implications of Green’s genocidal policies, before Greaves hands him a disk containing a status report on the Vulcan-Human child’s condition : she’s totally healthy. After Greaves leaves, Paxton self-administers a hypodermic injection to his neck.
Mayweather and Brooks’ tour ends up in launch bay 1. When asked by the reporter which of the shuttlepod he used to penetrate a sphere in the Delphic Expanse, he replies that it was Shuttlepod 1. The two open the shuttlepod’s hatch and go inside. Mayweather remarks that the crew is using the shuttlepods less and less due to everyone becoming comfortable with the use of the transporter. Mayweather remarks that when he saw Brooks at the conference earlier, he began to rethink some of the decisions he had made in his life. When she makes a joke about him now beginning to open up to her, he chides her for it. She tells him it is one of her bad habits and then suddenly kisses him. She admits another bad habit of hers is being unable to hide her attraction to someone.
In a conference room, the crew discusses Khouri’s autopsy from her case file. Phlox has found levels of growth hormone containing traces of myofibrilin, used in the Orpheus mining facility, a hotbed of Terra Prime activity. Reed says Mayweather has “a friend” in the Orpheus facility who may be able to smuggle in an undercover team; T’Pol and Tucker volunteer for the mission.
At the same time, on the Moon, miners remove rocks from what looks like a cave-in, and find Mercer’s body buried beneath.
Tucker and T’Pol search the mining tunnels on the Moon. They get lost, and Trip picks a new tunnel to explore just because he doesn’t recognizes it. T’Pol informs him that she knows of his doubts. Tucker assures her that he never said he didn’t believe her, but she just knows. Trip remarks that he is tired of their boud, which make T’Pol aware of everything. As they continue arguing, T’Pol notes the entrance to quadrant 3.
In Mayweather’s quarters, his relationship with Brooks takes a steamy turn. They are in bed together, although Travis’ mind is worrying about the away team. As he’s not allowed to talk about it, they change the subject, and discuss life goals; Mayweather considers settling down, believing that another challenge for him to face may be staying in one place for a change.
On the bridge, Sato informs Reed of a glitch in the universal translator system, but she can’t find it.
Back at Orpheus, Josiah introduces himself to Tucker. They begin discussing about the presence of aliens and how they will finish by taking earth over. Josiah invites Trip to a Terra Prime assembly that night.
T’Pol joins Tucker and tells him of Mercer’s death and of his connection to Susan Khouri.
Later, at the Terra Prime meeting, Josiah gives a xenophobic speech in front of an small assembly, He refers the Xindi attack and the bombing of the Earth Embassy on Vulcan and uses that as arguments against the coalition being formed.
T’Pol investigates the cave in where Mercer’s body was found, but she is shot by a phaser. Greaves gets out of the shadow, he’s the one who shot.
At the meeting, Josiah accuses Starfleet and the Earth government of not doing anything. He argues that they need to send the government a message, and that someone is here to help them do just that : commender Tucker, of the starship Enterprise.
On the ship, Brooks is placed under arrest for spying – Archer and Reed reveal to Mayweather that they have reason to believe that she’s a member of Terra Prime.
Tucker and T’Pol’s are taken hostage by members of Terra Prime. In Paxton’s office, he compares Tucker and T’Pol to Romeo and Juliet. He wonders if their “drama” will end happier than the suicide that Romeo and Juliet committed inside a medieval tomb. Tucker demands to know who Paxton is; he reveals that he is in charge of the facility and that he leads the Terra Prime movement. He tells Tucker and T’Pol that the child is alright – finally sleeping through the night. He also declares that his ultimate goal is to return Earth to its “rightful owners”, giving it back to human beings.
Paxton orders Greaves to take the facility to launch mode. The whole building starts shaking. When Tucker asks Paxton where their destination is, he tells the engineer that “this will be like a walk across the street” for him. The enormous mining facility launches off of the Moon’s surface.
Back on Enterprise, Brooks is being interrogated by Archer and Reed. Archer notes that her universal translator was reconfigured to record the alien delegates at the conference. Brooks denies doing anything wrong but Archer notes that, during a background check, they discovered that she had made three trips to the lunar colony in just the last month. She claims she was on assignment from her editor but Reed reveals that her editor never sent her there for a story. Archer asks her if she knows if Tucker and T’Pol are in danger; but she demands to speak to legal counsel. Archer angrily orders she be taken to the ship’s brig and given whomever she requests. Archer tells a visibly hurt Mayweather that he’s sorry. Just then, Archer is paged over the intercom. An officer tells the captain that the Orpheus mining facility has taken off of the surface of the Moon.
Later, when the facility is in open space, Paxton reveals to Tucker and T’Pol that Orpheus is actually a warp-capable vessel. Tucker says they’ll be lucky if the facility does not tear itself apart at warp but Paxton says he plans on luck. With that, the facility proceeds to warp and flies to Mars. Archer orders a pursuit course and tells Oshi to inform Starfleet that Enterprise is going after it. The facility lands on the surface of Mars. Terra Prime seizes control of the verteron array on the red planet, normally used to redirect comets, and uses it to fire a blast of verteron energy at Luna as a demonstration. Paxton issues a demand via subspace radio for all non-Humans to leave the Sol system. On the screen, he addresses the planet : “As of this moment, mankind casts off the shackles of alien interference and now determines its own fate… its own destiny. Terra Prime forever.” Archer stares at the viewscreen, uncertain what to do next.