A ship feeding off the Enterprise's warp field is exposed after the crew ignites the plasma exhaust. Commander Tucker takes a trip to the ship to help them repair their warp drive. After his return to the Enterprise, he finds some unexpected developments both on and inside his body.
In the Mess Hall over breakfast, Phlox tries to tempt T'Pol to eat blueberry pancakes rather than her traditional Vulcan Plomeek broth. T'Pol comments that it is difficult enough having to smell human food, let alone eat any. T'Pol's replicator request for carbonated water emerges as a viscous liquid.
In Engineering, Trip is trying to solve ship-wide problems with power supply and life support. The plasma exhaust has had its flow restricted by something, causing feedback in ship systems. Archer arrives and asks if it would be better to drop out of warp. Trip asks for a minute to solve the problem; just then a fire starts behind Archer, who puts it out with an extinguisher. Trip sighs and signals the Bridge to go to impulse.
T'Pol discovers a distortion in the plasma wake of the Enterprise. Archer plans to ignite the plasma waste to illuminate the problem. The blast reveals a cloaked ship. Archer hails the vessel and Hoshi programs the Universal Translator to interpret their language. Xyrillian Captain Trena'l explains that they have been tapping the Enterprise's plasma wake to recharge their engines and that they mean the humans no harm. Archer asks them to decloak and offers engineering assistance.
Trip is injected with 40mg of mirazine by Phlox to cut the decompression time in half to three hours. Trip is to stay on the Xyrillian ship for three days until the repairs are completed because of this. T'Pol urges Trip to be diplomatic. Later, Mayweather docks the shuttlepod and Trip goes aboard. Trip is surrounded by an opaque gas that burns his lungs in the decompression chamber while the Xyrillian Ah'len requests that he breathe normally.
The decompression ends, eventually, and Trip enters the Xyrillian ship. His perceptions are altered, with sound slowing down and vision hazy. Trip ignores the advice of Captain Trena'l to rest and goes to Engineering with Ah'len, passing tanks of alien cetaceans on the way. Engineering is a confusing environment of noise, bright flashing lights and alien technology. Trip has trouble concentrating. He speaks to Archer who orders Trip to get an hour's rest on Trena'l's advice. Ah'len takes Trip to rest.
When Trip awakens, Ah'len feeds him. When they touch, sparks literally fly between them. Later, Trip communicates with Archer and T'Pol as he works on the Xyrillian engine. As he works, he comments favourably on the ship. The teraphasic coils take an hour to recharge, so in the meantime, Ah'len takes Trip to a holodeck to show him Thera, the Xyrillian homeworld. Ah'len changes the environment from a sandy plain to a boat on a body of water. Ah'len asks how humans detect moods without dermal plating and why Trip is growing stubble. As she touches his face, more sparks fly. She summons a game consisting of a bowl of white granules. They put their hands in to the crystals and Ah'len amazes Trip by telling him that his favourite food is Catfish. Trip is even more amazed when he finds that he can do the same. Engineering signals that the coils are coming back online, so Ah'len ends the game and shuts down the holodeck.
Trip returns from the Xyrillian ship, enthusiastic about his encounter with the new race. Trena'l and Ah'len say farewell to the Bridge crew on the main viewer. Later, Trip and Reed are eating in the Mess Hall. They laugh over the possible uses of a holodeck, if one existed on the Enterprise. Trip eats enthusiastically, then notices a strange growth on the inside of his wrist. Trip visits Phlox, who enquires if Trip had intimate relations with a Xyrillian. Phlox scans Trip and finds the blastocyst between his sixth and seventh intercostal ribs - the growth on Trip's wrist is a nipple. Phlox tells a stunned Trip that he is pregnant.
Phlox tells Trip, Archer and T'Pol that the Xyrillians only utilise maternal genetic material in reproduction, the males acting as hosts. T'Pol can't believe that Trip couldn't conduct himself in a proper fashion for three days. Trip defends his behaviour. Phlox can't remove the embryo without risking both of their lives. Trip mentions the telepathic game that he and Ah'len played and Phlox says that it might be the transfer medium for the genetic material. Archer asks T'Pol to locate the Xyrillian ship in order to remove the embryo.
Trip resumes his duties in Engineering. He steps out of the lift and complains about the safety hazards that it presents for a small child.
Later, Trip enters the Mess Hall in a loose-fitting shirt. He looks around at the crew suspiciously before joining Archer and Phlox in the Captain's Mess. They deny having mentioned Trip's pregnancy to anyone, so he assumes that T'Pol broke the secret. Trip shows that he is growing a third nipple on his wrist. Archer and Phlox prepare Trip for the worst case scenario, that he will have to deliver and raise the child as his own if they can't find the Xyrillian ship. Trip doesn't want to become a working mother. The gestation period will only last another six weeks at most. Archer tells Trip to look on the bright side - this is the first interspecies pregnancy involving a human.
On the Bridge, Reed detects the Xyrillian ship; T'Pol changes heading to intercept. When they approach, they discover that the ship is a Klingon battle cruiser.
The Xyrillian ship is hiding in the Klingon ship's plasma wake. Archer hails the Klingon ship, which turns, targets and fires two warning shots. Archer hails again and asks Captain Vorak if they have been experiencing any technical problems. Vorak says yes; they detect the Xyrillian ship when Archer informs them, then lock on with a tractor beam. Vorak orders Trena'l brought to him and that the crew be executed. T'Pol interrupts to tell Vorak that Archer is the man who found Klaang and saved Qo'nos from civil war and that the Chancellor himself called Archer brother in the High Council Chamber. Archer convinces Vorak to take Trip to the Xyrillian ship. Vorak refuses until Archer informs him of Trip's pregnancy.
Vorak and his second officer go with Trena'l to see the holodeck recreate the capital of Qo'nos. Vorak is impressed by the holodeck demonstration - he can even see his own house from their vantage point. Trip shows Ah'len the pregnancy; she is amazed that it could happen with another species. She scans the embryo and announces that it can be safely transferred to another host. The baby girl looks very healthy.
Back on their ships, Vorak ends the encounter by stating that the debt to Archer is repaid and that Archer will regret meeting the Klingons if they ever cross paths again. Later, in the Captain's Mess, Archer asks T'Pol if the Klingon Chancellor called him brother. T'Pol replies by saying that Klingons are known to exaggerate, so she saw nothing wrong with doing the same. T'Pol tells Trip that his pregnancy is the first recorded instance of a human male pregnancy. "Just how I always wanted to get in to the history books", says Trip.