T'Pol and Trip study the alien's pod and come to the conclusion that the alien was placed in the spatial anomaly so that someone could keep track of his exposure to the environment — he's a test subject. The pod's hull also contains the same combination of alloys found in the surface of the Expanse's mysterious spheres. As the mystery grows, Archer insists on questioning the alien further. The alien, however, won't reveal much and just claims he is from a trans-dimensional realm and that he's a prisoner participating in an experiment he knows nothing about.

Meanwhile, long-simmering tensions among the Enterprise crew begin to boil over. T'Pol learns that Trip has been holding Vulcan neuro-pressure sessions with MACO Amanda Cole and is surprised to find herself distracted by the situation. When she confronts Trip about it later, the two finally give in to their mutual attraction and consummate their relationship. Also, Major Hayes convinces Archer to allow the MACOs to put the ship's security team and senior officers through a series of training drills. Reed, who has resented Hayes' presence from the beginning, feels that his authority is being challenged. The two become increasingly combative during the training sessions and end up engaging in a full-out brawl.

Back in Sickbay, the alien's condition seems to be taking a turn for the worse. As soon as Phlox turns his back, however, the alien attacks him and disappears through the wall, into the ship. As the alien disrupts systems throughout the ship, the crew frantically attempts to track him down. They eventually realize that he's headed for Engineering. Reed and Hayes — putting aside their differences for the moment — race to Engineering and find the alien plunging his arm into the warp reactor. The two men work together to trigger a feedback response that blasts the alien, and he is knocked to the ground, unconscious.

Later on, Archer chastises Hayes and Reed for their juvenile behavior. The two men seem to have come to a sort of understanding, however, having worked together so successfully to stop the alien. Meanwhile, T'Pol and Trip are forced to deal with the awkwardness that follows their intimate encounter. T'Pol coolly thanks Trip for his help in her "exploration of human sexuality" and the two agree to forget that it ever happened. They do, however, decide to continue their neuro-pressure sessions.

In Sickbay, the alien is drawing his final breaths. Archer demands to know why the alien tried to destroy Enterprise, but the alien can only offer cryptic, chilling last words: when the Xindi destroy Earth, he says, his people will "prevail." With that, he disappears, leaving Archer with even more questions than before.