Hoshi and Trip are surveying some primitive alien ruins, taking pictures and discussing what might have happened to the people who used to inhabit the planet. Suddenly, Archer contacts them and asks them to return immediately to Enterprise — a storm is heading their way. As the duo prepares to board their shuttlepod, Archer contacts them again. The storm situation is more urgent than he predicted, and he needs to bring Trip and Hoshi up via the transporter, one at a time. Hoshi is apprehensive, and insists that Trip go first. Once he is safely onboard, she beams up.
Back on Enterprise, Hoshi feels strange, but decides that she just needs some rest. Later on, she joins some of her crewmates for a meal — strangely, they seem to be ignoring her the whole time. Dr. Phlox insists there's nothing wrong with her, however. The next day, Hoshi is summoned to the bridge — Trip and Mayweather have been taken hostage by aliens while attempting to retrieve Enterprise's shuttlepod. Archer needs Hoshi to decipher the aliens' language. Hoshi, however, can't seem to accomplish her task, and a frustrated Archer sends her back to her quarters and assigns her duties to Crewman Baird.
Later, Hoshi learns that Baird deciphered the language easily, and the two officers were returned safe and sound. Also, Hoshi is to remain off-duty for the time being — Baird will assume her responsibilities. Feeling useless, Hoshi begins to notice more troubling signs: water in the shower seems to pass right through her, and the turbolift does not respond to her. Also, she seems to be hearing strange voices. Distressed, Hoshi pays another visit to Phlox ... who maintains that there's nothing wrong with her.
Still apprehensive, Hoshi heads to the gym to work out. Soon, however, her hands pass right through the free weights and the doors will not respond to her. Upon looking in the mirror, Hoshi discovers that she has become completely transparent. The crew soon discovers that she is missing and mounts a search. Though she is invisible to them, Hoshi trails the crew, hoping to somehow send them a message that she's still alive. The crew, however, determines that Hoshi's disappearance is, in fact, connected to a transporter snafu — apparently, her molecules are breaking down. In her invisible form, Hoshi also makes a disturbing discovery — aliens have infiltrated Enterprise and are planting explosives that will soon detonate. Desperate, Hoshi tries to contact the crew, resorting to such tactics as Morse Code. Nothing seems to work, however.
Eventually, Hoshi sees the aliens heading towards a transporter pad, taking the detonator for the explosives with them. Quickly determining that the only thing she can do is follow them, she overcomes her fear and leaps onto the transporter pad. As she begins to hear voices again, she suddenly finds herself materializing on Enterprise. The voices belong to Trip and Reed, who are in the process of beaming her back. The mysterious aliens have vanished.
Reed and Trip inform Hoshi that she was trapped in the pattern buffer for a few seconds ... leading Hoshi to conclude that the whole ordeal took place in her head, while she was being transported from the surface. Relieved, Hoshi gets a quick check-up from Phlox, and informs Archer that she'll stick to shuttlepods for the time being.