Enterprise encounters a large, otherworldly vessel unlike any the crew has seen before. They try to make contact with it, but to no avail. Suddenly, a large portal opens and the ship "swallows" Enterprise, rendering its weapons and engines useless. Luckily, life support is still operational. Archer, Trip and Reed take a shuttlepod into the cavernous ship for further exploration. Although there doesn't seem to be any immediate threat to Enterprise, Trip is suddenly attacked by a colorful wisp of smoke that seems to invade his body for a few seconds before releasing him. Back in Sickbay, Trip insists that he's fine. He explains that during his brief encounter with the alien wisp, he had an out-of-body experience and believed he was in Florida and visiting an old girlfriend.
Archer is perplexed, to say the least. He orders Trip to get the engines back online, then discusses the situation with T'Pol. Though Archer believes that their captors have hostile intentions, T'Pol cautions that there's no reason to believe these mysterious aliens mean Enterprise any harm. Suddenly, Archer and T'Pol are contacted by a crewman who informs them that Trip is acting strangely. They find the commander in the mess hall, devouring large amounts of food and speaking in an odd manner. Archer deduces that Trip has been overtaken by another being, and attempts to communicate with it. The alien informs Archer that Trip is exploring another realm while the alien explores humanity. Archer insists that Trip and Enterprise be released. The alien complies, and the giant alien vessel releases Enterprise while the alien lifeform leaves Trip's body. A dazed Trip tells Archer that his exchange with the alien made for some amazing experiences and that the aliens told him that anyone on the crew was free to try a similar exchange. Archer, however, is still skeptical, and is determined to get Enterprise away from the area as soon as possible. Unfortunately, engines are still down.
As the crew works, more of them are suddenly invaded by the strange, noncorporeal beings. Reed is overtaken and attempts to mate with T'Pol, while Hoshi is invaded and tries to incapacitate Dr. Phlox. As more and more crewmembers are overtaken, Archer realizes that Enterprise cannot leave the area until the crew is returned to normal. While Phlox works on a solution, Mayweather is chased into the catwalk by one of the wisps. When the wisp doesn't follow him, he realizes that the area must contain a component that keeps the alien beings out. Upon hearing this, Archer orders all unaffected crewmembers to the catwalk.
Once there, Archer and T'Pol discuss options for saving the crew. T'Pol has an idea: she wants to allow one of the aliens to enter her body so that she can learn the intentions of the beings. She insists that the highly-evolved Vulcan mind should be able to resist being overtaken. Once T'Pol leaves the catwalk, she immediately encounters one of the wisps. She is able to resist invasion, but learns that the beings have been lying to Archer. Their ship is deteriorating and they need corporeal bodies in order to survive. With this in mind, Archer hatches a plan — he will send Phlox (whose biological make-up is incompatible with the aliens) to release carbon dioxide into Enterprise's living quarters, rendering the affected crewmembers unconscious. Once that happens, the aliens won't be able to survive and will leave the crewmembers' bodies. Phlox carries out Archer's orders, but meets an unexpected foe: Trip, who has been overtaken once again. Luckily, Phlox manages to release the gas, which knocks Trip out. The wisps vacate the crewmembers' bodies and Enterprise takes off with the alien ship in pursuit. Enterprise fires torpedoes, which detonate and destroy the vessel for good.