While at warp speed, a huge alien vessel overtakes and swallows Enterprise, disabling the ship's engines and weapons in the process. When the scanners register neither the alien ship nor its numerous energy-wisp-like non-corporeal beings, Captain Archer takes Lt. Reed and Commander Trip Tucker on an away mission to the interior. While EV Tucker is visibly "entered" by one of the beings before being returned to his normal state, albeit with random memories of having been on Earth. Dr. Phlox's examination however reveals no ill effects for the experience.
Later, Tucker is possessed again, and is soon located in the mess hall enjoying the simple pleasures of food. The alien says that they are explorers who merely want to experience the tangible nature of the corporeal state they long evolved from. In exchange, the crew would be permitted to have the chance of out of body experiences. Archer, doubtful and unconvinced of the aliens benign intentions, demands the release of his ship, and the return of Tucker's consciousness—which quickly happens. The Enterprise is again freed and floating in space, but the engines are still not operational.
While affecting repairs, one-by-one the crew-members start acting out of character and displaying signs of possession, including Reed who enters Sub-commander T'Pol's quarters and suggests she disrobes so that he may experience "coupling". Similar events occur throughout the ship, including the takeover of Ensign Sato and 22 others. Ensign Mayweather, himself escaping a pursuing entity, discovers sanctuary in the nacelle catwalk area, so Archer moves the non-infected crew back onto the cramped safety of the engines. While there, T'Pol proposes a plan that she will use her more disciplined mind to try to uncover the beings' intentions instead of being infected by them. Archer is opposed to this dangerous plan, but conceded given that there is no other alternative.
T'Pol is soon overcome and discovers that the aliens plan to co-opt the 82 crew-member's bodies to save themselves from their failing ship. Archer, T'Pol and Phlox soon hatch a plan to forcibly expel the beings by asphyxiating the infected crew. Though he has some trouble with an infected Tucker, Phlox is able to reach the atmospheric controls and floods the ship with CO
2, and the aliens are forced to return to their ship. When the alien ship attempts to pursue and recapture the Enterprise, Archer destroys it with two torpedoes.