Two weeks into their first mission of deep space exploration, the Enterprise crew is still breaking in their ship and itching for first contact with another civilization. Captain Archer hears squeaking; Lt. Reed tests his weapons system on an asteroid field; Ensign Sato is trying to keep an alien slug alive; Commander Tucker tries the resequenced protein food; and Dr. Phlox is intrigued by human behavior. Sub-commander T'Pol detects a ship floating immobile in interstellar space, so Captain Archer decides to try to make contact with it. Getting no response, the crew takes a closer look at the alien vessel and sees evidence of weapons fire, and bio-scans reveal lifeforms with very low cellular activity. Over T'Pol's protestations, Archer orders Reed to prep a shuttle, and asks an apprehensive Hoshi to come along.
The shuttlepod carrying Archer, Reed and Hoshi docks with the alien ship, and the away team — in environmental suits — boards the vessel. The ship's interior looks old and worn, the nitrogen-methane air is below freezing temperature, and the walls and floors are stained with a blue-green liquid that appears to be blood. They follow a noise into a large bay where they find hydraulic machines. When Hoshi shines her beacon on one of the machine conduits and follows it up the wall, she sees something above her and screams. Alien bodies are hanging from the ceiling with tubes draining their fluids.
Back at Enterprise, Archer concurs with T'Pol that whoever killed the aliens will likely come back and put their own crew in jeopardy. The ship resumes course, but Archer is plagued by guilt for abandoning the victims without at least trying to contact their people, so he orders Ensign Mayweather to turn back. Back onboard the alien cargo ship, Hoshi works with Trip to repair and decipher the communications consoles and send off a distress signal in the aliens' own language. Performing an autopsy on a corpse, Dr. Phlox learns that the alien crewmen were being drained for triglobulin, a valuable fluid that can be used to create medicines, vaccines and aphrodisiacs. But the away team has to evacuate when a vessel approaches with a power signature matching that of the perpetrators' machinery.
As the shuttlepod returns to Enterprise, the hostile vessel fires and knocks out the starship's port nacelle. Reed fires two torpedoes, but they are useless against the enemy ship's superior defenses. The bridge crew then finds themselves being probed by a bio-scan which no doubt reveals to the attackers that the human lymphatic system contains some, in Dr. Phlox's words, "useful compounds." Just then another vessel drops out of warp and hails Enterprise. This alien captain is from the same species as the murdered crew, apparently responding to Hoshi's distress call. Hoshi tries to communicate with him through the computer translator, but its inaccuracy causes the alien captain to think the humans were responsible for the murders. As the enemy ship prepares to drill through the hull and board Enterprise, Hoshi abandons the translator and begins talking to the alien captain directly as best she can in his language. Despite the extreme pressure she's under, Hoshi manages to convince the alien captain of their friendly intentions, and he begins to attack the other vessel. While the enemy ship is vulnerable, Reed fires another torpedo and causes some serious damage, and another shot from the alien captain finishes it off.
The Enterprise crew learns their new allies are called the Axanar, and after helping them recover their dead crewmen they spend some time on their planet. Before resuming course, Archer agrees to a brief detour to allow Hoshi to place her slug on a new planet — not exactly like home, but close enough to adapt to and do just fine, similarly to Hoshi's own experience of adjusting to life aboard Enterprise.