This is a summary of the beginning portion of the episode. Please note that the events described in this summary are not necessarily in the same chronological order in which they occur on screen. While traveling through the Delphic Expanse, the Enterprise encounters a trans-dimensional disturbance that lies directly within its navigational course. The crew learns that the disturbance causes permanent neurological damage to humans who are exposed to its interior. Apparently, the neurological risk to Vulcans is similar. To avert the danger, an idea to have Phlox disable the neo-cortices (presumably a part of the central nervous system) of all crewmembers, except himself, is deliberated among the senior officers. In this plan, the entire crew (except Phlox) would effectively be tranquilized until Enterprise was clear of the dangerous disturbance. Thus, the neurological danger to the crew would be neutralized. Furthermore, during that time, all responsibility for the well-being of the ship and the crew would lie with Phlox. The only alternative to this plan, as decided by the senior officers, would be to circumvent the disturbance altogether. This is felt to be too time-consuming, however, and despite Tucker's skepticism, the former plan is implemented.
While the crew is soundly resting, Phlox is shown attending to his duties aboard the ship. With a lack of inhibition, he even on occasion fails to clothe while doing his work. (The entire episode is also superimposed with Phlox's composition of a letter to an acquaintance of his.
Unfortunately Phlox himself begins to hallucinate. In his first series of apparitions, he is frightened by what he perceives as strange sights and sounds, and he frequently assumes he is sensing other people in his vicinity (though everyone else aboard the ship is asleep). Phlox's delusions escalate when he is accompanied by an imaginary T'Pol. Phlox, and the audience for that matter, believes she is real; it is revealed only at the end of the episode that this isn't true. In fact, at this point, the audience is unaware that any of Phlox's perceptions are false; the audience experiences as legitimate all of the events that take place in Phlox's mind.
As the episode progresses, however, the audience is falsely led to believe that T'Pol was excluded from Phlox's treatment, and that she is accompanying him in administering to ship-related duties while they venture through the disturbance. Phlox sees something on the hull and later, an enemy Xindi. Both times, the 'T'Pol' reassures him there is nothing there.
Unconvinced, Phlox takes it upon himself to solitarily search the ship, deck by deck, for Xindi, with a deadly phase pistol in hand. He almost kills, Porthos, who Phlox earlier left unsecured and unattended.
It is revealed within the episode that Denobulans, the species of which Phlox is a member, frequently do hallucinate under periods of stress and prolonged isolation. However, unlike humans, such hallucinations are not signs or symptoms of insanity and mental collapse, but rather a normal part of their biological adaptation to stressful situations. The mind provides itself with figures of conversation so that, despite being isolated, it may remain occupied and focused.