Trip and Sato examine archaeological ruins on a planet that is otherwise lifeless. Due to an energy storm on the planet, returning to the Enterprise is imperative. Since the shuttle pod is too risky, the transporter will be used. In order to assure Hoshi that it's safe for humans, Trip goes first.
When Hoshi is beamed on the Enterprise, she feels not quite right. She sees her reflection in the mirror fade, water in the shower goes through her hands, and the crew doesn't always notice her presence. She sees Phlox twice, but he gruffly assures her that she's fine - it's all in her head.
Tucker and Mayweather return to the planet to retrieve the shuttle pod. They are captured by aliens and Hoshi is called to the bridge to translate. She fails, and is relieved of duty. A less competent officer translates the language, and Trip and Travis are freed. After discussing this with Trip, Sato is trapped in the gym when she becomes non-solid. Though the crew looks for her, she can't communicate with them -- which she needs to do as there are aliens on board planting explosives. She does what she can to foil their plan... even going so far as to jump onto their portable transporter pad.
Hoshi then materializes in the Enterprise's transporter room only seconds after the transport started from the beginning of the show. All of Hoshi's memories are little more than a pattern-buffer-delay-induced hallucination.