Ensign Hoshi Sato passes through the transporter and finds that she is disappearing. At the same time, she is the only person who can see aliens planting explosives in key ship systems, with no way to warn the crew.
Ensign Hoshi Sato and Commander Trip Tucker are on an away mission, taking pictures and gathering data and samples from an ancient set of ruins. Their mission is cut short, however, when a diamagnetic storm approaches. But before they can make it back to the shuttlepod, another storm closes quickly and they are forced to use the transporter instead. Hoshi is reluctant to use it, so Trip goes back first.
After the incident Hoshi feels that things are not right, particularly being the first time she used a transporter. After a visit to the doctor, she goes to sleep, hoping to feel better in the morning. She is wakened by an emergency call from the bridge having apparently overslept by three hours. On the bridge, Captain Archer informs her that Trip and Ensign Mayweather have been taken hostage on the planet while retrieving the shuttlepod. Hoshi is unable to help, failing to understand the "simple bi-modal syntax" of the aliens. She is ordered to return to her quarters, where she sees her reflection in the mirror fade away and water passing through her hands when she takes a shower.
After another visit to Sickbay, Dr. Phlox still cannot find anything wrong, attributing Hoshi's experience to transporter anxiety. But only a little while later, when in the gym, Hoshi completely dematerialises, still conscious but unable to interact with her environment. Later, the crew begin to search for her and she then follows them around the ship. She observes Phlox and Tucker scanning the ship for her residue. She watches Archer speak with her father to inform him of her "death", and sees her attempt at morse code fail too. She also learns that the initial problem was in the transporter itself, confirming her initial theory.
In her wanderings, she hears and later encounters two strange aliens who are planting and arming suspicious devices throughout the ship. Unable to warn anyone, she endeavours to save the ship herself, and tries to interrupt the devices. This eventually leads her to step onto an alien transporting device - which mysteriously takes her back to her initial away team return in the transporting room. She is disoriented, and concerned about the aliens, but Lt. Reed explains to her that she has been trapped for 8.3 seconds in the pattern buffer because of the storm, and that all her recent experiences were only hallucinations.