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In another flashback, T'Pol is speaking with Ambassador Soval. He wants her to return to Vulcan with Archer. Soval blames the humans for what has happened but T'Pol reminds him that it is the Vulcans who held them back and that if they hadn't, the humans might have been able to defend themselves. T'Pol wants to stay with Enterprise and Soval tells her: "Your emotional attachment to Archer is clouding your logic." T'Pol goes to Archer's quarters and he tells her he saw the Vulcan ship and asks what they wanted. She tells him they were there to replenish their supplies. Archer wants more to do but she tells him it's been tried before and didn't work out well.
T'Pol continues to tell Archer what has happened, that there were several convoys of colonists that tried to make it to Ceti Alpha 5 but only the one led by Enterprise made it. In another flashback, T'Pol tells Trip she will resign her commission and that Archer will be better off with the colonists and that she will take care of him. Back in the future, she tells Archer that at that point he usually starts thinking he's being deceived. She tells him something about his life that is very personal to qualm his doubts.
Meanwhile, a shuttle arrives at the colony with Phlox on board. He visits Archer and examines him. He tells him that the only way to cure him according to Denobulan scientists would have been to blow him up in a subspace implosion. Then he says he has found a less extreme way to cure him but that they need the energy from a warp engine and that means they have to go to Enterprise.
They go to the ship and meet up with the crew. Trip and Reed have been promoted to captain. Hoshi is there as well. They go to engineering and Phlox tells him they will be ready in an hour. Later T'Pol visits Archer in his quarters. He had left the reception early as he was uncomfortable. Archer thanks T'Pol for all her help over the years. Phlox calls Archer to tell him they are ready.
While Archer is undergoing the treatment, Reed picks up a duranium signature near the sun. He's unsure if it is a ship. Trip lays a course to investigate. Phlox succeeds in destroying one of the parasitic clusters in Archer's brain. Meanwhile, Enterprise intercepts a small vessel. The small ship tries to leave but it is stopped by Enterprise and they bring it into the launch bay. Back in engineering, Phlox talks to T'Pol about her life with the captain and how it must have been hard for her. He intimates that she is attached to Archer. In the meantime, she finds a discrepancy in the scans.
In the launch bay, Tucker and Reed interrogate the only passenger of the small vessel who is an Irydian. He says he was waiting for a buyer for his flamegems but Reed tells him that Irydians are information dealers. After Trip threatens to destroy his ship, the alien tells them he was watching Phlox and that the people who hired him wanted to know wherever he travelled presumably to find out where the human colony was.