Enterprise is still undergoing repairs, but Captain Archer is determined to make it to Degra's rendezvous point on time. The crew, however, is still reeling from the loss of the 18 crewmen who died during the Xindi attack. The loss seems to be hitting Trip especially hard, particularly when Archer orders him to write a letter of condolence to an engineering crewman's family. T'Pol, meanwhile, is dealing with problems of her own — she's coping with the lingering effects of her trellium addiction, and is finding her emotions difficult to control. Phlox points out that the addiction caused serious damage to her neural pathways. She may have to learn to live with these emotions.
Enterprise finally meets up with Degra, who leads them inside a nearby Sphere cloaking barrier. He then invites Archer onto his ship to meet with him and the Xindi-Arboreal from the Council. Degra explains that he was the one who arranged for Archer to be returned to Enterprise. He also called off the Xindi attack on the ship. Degra goes on to reveal that the Xindi weapon is set to be launched in a matter of days — if the Xindi are to believe Archer's story, they need proof and they need it soon. Archer brings Degra and the Arboreal onboard Enterprise and shows them his evidence — the Xindi-Reptilian corpses he and T'Pol recovered from their time travel mission to Detroit, as well as a sample of the toxin the Reptilians planned on using against Earth's population. He also shows them the information Enterprise collected on the bizarre trans-dimensional "test subject" they encountered — which Archer believes was of the same species as the Sphere-Builders. Archer uses the evidence to deliver his point: humans and Xindi are destined to form an alliance to stop the Sphere-Builders. If the Xindi attack Earth, it will never happen. Both species will be destroyed.
Meanwhile, the ship's hull has ruptured and is spewing a steady stream of plasma. To repair it, Trip and Malcolm Reed don EV suits and head out to the hull, hoping to get close enough to the malfunction to fix it. They're successful, but Reed collapses from the heat. Phlox rushes him to Sickbay and Degra, who has been observing, expresses concern for the injured officer. Trip, who has barely been containing his resentment towards Degra and the other visiting Xindi, lashes out — the Xindi had no problem killing seven million humans, he says, but one is more than they can handle? Trip continues his tirade, but Archer steps in and orders him to cool off.
Later, Degra and Archer discuss their respective research on the Delphic Expanse's Spheres. Archer apologizes for Trip's behavior, but Degra assures the captain that he understands. The two continue to talk, and seem to be forging a bond. Degra expresses hope that Enterprise will one day be able to return to its mission of exploration.
Suddenly, Enterprise is approached by a Reptilian ship — somehow, they've found Degra. Enterprise can't beat the Reptilian ship alone, soArcher insists that Degra has to help them. Degra is aghast at the idea of attacking other Xindi, but he knows their ship's vulnerabilities and realizes it has to be done. He assists Enterprise in disabling the Reptilian vessel ... and then fires again and obliterates it. Archer is somewhat shocked by this, but Degra tells him the action was necessary — otherwise, the Reptilians would have contacted the Council and the alliance he has forged with Archer would have been lost.
Later, back on Enterprise, Degra comes up with a proposal: Archer must speak to the Xindi Council. He believes that Archer's evidence will force the Council to take him seriously. He gives Archer the coordinates of the Council chamber, but since it would take Enterprise weeks to get there, he also provides the location of a subspace corridor that can serve as a shortcut. In the meantime, Degra (who has a much faster ship) will do everything he can to stop the launching of the weapon. Cautiously hopeful, the two men shake and agree to meet in three days.
Meanwhile, Trip is struggling with the losses he's experienced. He tells T'Pol that even though he's supposed to be writing a letter to the family of Crewman Taylor, he can't help but dwell on Elizabeth, his kid sister who was killed in the Xindi attack on Earth. T'Pol manages to comfort him and helps him come to terms with the difficulty of the past few months. Later, Trip is able to write the letter, and in doing so, finally says good-bye to his sister.