A rash of odd malfunctions are afflicting the Enterprise NX-01, such as a gravity outage while Captain Archer is showering. Chief Engineer Tucker determines that the ship's plasma exhaust flow is being restricted for some unknown reason. When Archer orders Lt. Reed to ignite the plasma exhaust, they discover a cloaked alien ship riding between the ship's nacelles.
Archer hails the "hitchhikers" and learns their engines are malfunctioning and they've been using Enterprise's exhaust to replenish them. Archer offers to help them with repairs, so Tucker prepares for a three-day away mission on the disabled ship. Tucker has to undergo a very uncomfortable three-hour decompression and acclimation process, and when he enters the Xyrillian ship, he is faced with a disorienting visual and auditory experience — the walls are glowing with bioluminescent moss, the consoles operate with viscous fluids and electrical arcs, there's an aquarium holding hundreds of undulating eels, and the Xyrillians themselves glisten with moist, scaly skin. Tucker insists on going straight to work in their engine room, but he has a very hard time adjusting to the environment. After finally agreeing to get some rest, Tucker starts to enjoy his stay, and develops a flirtatious friendship with the female engineer, Ah'len. On a break from their repair work, Ah'len shows Tucker a holographic chamber where she recreates a three-dimensional landscape of her homeworld. While sitting in a holographic boat in an exotic ocean, she introduces Tucker to one of their games: they immerse their hands into a box of granules which begin to glow, enabling them to read each other's minds.
After helping the Xyrillians get their teraphasic coils back on line, Tucker returns to Enterprise and the ships go their separate ways. As Tucker relates his experiences to Reed over lunch, he notices an unusual growth on his left wrist. He visits Dr. Phlox, who determines the growth is a nipple and he has an embryo forming in his ribs... Tucker is pregnant! Tucker insists to Phlox, T'Pol and Archer that he had no sexual encounters during his stay, but then realizes that the "box of pebbles" he shared with Ah'len must have inadvertently served as a medium to transfer genetic material. Phlox says the embryo is actually not his child, but that he is simply serving as a host, so Tucker hopes the lifeform can be removed from him and incubated. But Phlox is hesitant to perform any procedure without learning more about the Xyrillian gestation process, so Archer sets out to track down the Xyrillian ship, while agreeing to keep Tucker's condition secret from the rest of the crew.
Days go by as Enterprise looks for the Xyrillians, and in the meantime the bulge in Tucker's ribcage is growing while he experiences morning sickness, a ravenous appetite, and severe mood swings, which baffle his crewmates. After more than a week, Tucker has to face the possibility that he will have to deliver the baby and care for it. On the "bright side," Archer points out to Tucker's chagrin that he's making history with the first interspecies pregnancy involving a human.
Tucker is relieved when the Xyrillians' warp signature is detected, but upon approach, Enterprise comes face-to-face with a Klingon battle cruiser. Apparently the Xyrillian ship has malfunctioned again and they're hiding in the Klingons' plasma wake. Archer hails the Klingons and informs them about the stealth vessel. The angered Klingons intend to kill the Xyrillian crew, but Archer tries desperately to talk them out of it. Tucker steps forward and suggests that the Xyrillian crew would be willing to share their holographic technology if their lives are spared. The Klingon captain, Vorok, is enticed, but refuses to let Tucker join them as they board the ship. Archer then reveals that Tucker has some unfinished business involving a pregnancy, but Vorok holds firm. Tucker then grits his teeth and shows his "bulge," revealing he is the one who is pregnant and giving the Klingons an uproarious laugh.
Tucker and two of the Klingons board the Xyrillian ship, and after a decompression period, Tucker talks Trena'l, one of their leaders, into cooperating. Trena'l installs a topographical survey of the capital city of Kronos into the holographic chamber, allowing the Klingons to experience a simulation of their homeworld, and agrees to adapt the technology to the Klingon ship. Meanwhile Ah'len is surprised to learn about Tucker's pregnancy, unaware such a thing could happen with another species. She scans the embryo and determines it can still be transferred to another host, and learns it's a girl.
Captain Vorok informs Archer that the Xyrillians will soon be free to go, but when Archer extends his friendship to the Klingons, Vorok issues a stern warning that if they should ever meet again, he will regret it. On a brighter note, life for Tucker returns to normal again, except for knowing that he will go down in history as the first human male to become pregnant.