Following an extremely awkward first contact meal with an alien race known as the Kreetassans, Archer struggles to learn what offended his strange guests, while Hoshi works frantically to decipher their incredibly complex language. Unsuccessful at communication, Archer and Hoshi watch helplessly as the indignant Kreetassans return to their ship and disengage. However, the Enterprise officers do not see a fibrous, web-like creature propel itself along the Kreetassan hull, then leap into the Enterprise airlock just as the doors seal shut. Later, as she continues to work on deciphering the Kreetassan language, Hoshi becomes irritated with T'Pol — the Vulcan Sub-commander is trying to be encouraging, but Hoshi finds her analysis of the situation to be condescending. Before she has time to ponder this further, Hoshi notices strange frequency distortions coming from the com system. While they don't seem to be causing any problems, Hoshi informs Trip, who says he'll take a look at the problem in the morning.
Trip heads over to Archer's Ready Room — the chief engineer hopes to cheer his friend up with a tape of the Stanford/Texas water polo match. While enjoying the game, Trip and Archer suddenly receive a call from a panicked Crewman Kelly. Kelly has discovered a strange lifeform in Cargo Bay Two and informs the captain that the creature has captured Crewman Rostov. Archer, Trip, Reed and another security officer race down to the cargo bay, phase pistols ready. The four men are stunned to find Rostov and Kelly completely wrapped in the creature's tendrils. The two crewmen are alive, and Rostov warns Archer to leave. As they turn to go, the creature wraps its tentacles around Archer, Trip and the other security officer, and violently yanks them into darkness. Reed retreats, closing the door just in time to sever the small end of a writhing tentacle.
Reed, T'Pol, Hoshi and Mayweather meet and deduce that the organism must have come from the Kreetassan vessel. Mayweather works on locating the ship, while Dr. Phlox analyzes the organism's severed tendril. Phlox notes that the tendril appears to be capable of surviving independently, and that it possesses a sophisticated nervous system. Hoshi wants to try communicating with it, but T'Pol insists there isn't time, and suggests they neutralize the creature instead. Phlox notes that the creature is highly photosensitive — a sustained burst of EM radiation could potentially stun it. Surreptitiously entering the cargo bay, Reed and his security team strategically position themselves, and then fire the EM radiation at the creature. The organism writhes in pain, emitting shrieks of agony. However, when the bio signs of the trapped crewmembers become erratic, Phlox orders Reed to desist and withdraw. Phlox says that the organism appears to be absorbing the crewmembers' nervous systems into its own. If they keep firing on the organism, they could end up killing their own people.
As the creature bonds itself more permanently to the trapped crewmen, T'Pol has few options left and orders Hoshi to try communicating with the organism. Reed, however, is worried that the creature seems to be growing so rapidly, and suggests using an experimental EM forcefield to limit its growth. On the bridge, Mayweather finally locates the Kreetassan ship and lays in an intercept course. Desperately awaiting rescue, Archer, Trip and Rostov try to maintain their composure while wrapped in the creature's slimy tentacles. Strangely, the trapped crewmen begin to know each other's thoughts, indicating how close the symbiotic creature is to integrating them all into one being.
Meanwhile, Hoshi is exhausting herself trying to decipher the organism's bizarre language. Because the language appears to be something like a "calculus equation," T'Pol offers to lend her background in mathematics to the proceedings. Unfortunately, the two officers aren't getting very far, and Hoshi is increasingly frustrated — especially since she feels that T'Pol questions her judgment at every turn. Fed up with what she sees as constant criticism, Hoshi finally snaps at T'Pol — she thinks T'Pol doesn't believe she belongs onboard Enterprise. T'Pol responds that she actually has a very high regard for Hoshi's abilities ... and therefore holds the ensign to a high standard. Shocked at this revelation, Hoshi suggests a new tactic for deciphering the language and the two women go back to working together, determined to crack the mysterious code.
Back on the bridge, Mayweather is hailed by the Kreetassan captain ... who now speaks English! The captain reveals that the Kreetassans learned the language from the Enterprise database, and apologizes for unknowingly transferring the creature to Enterprise. The captain offers to send the coordinates for the creature's homeworld, but first Mayweather must apologize for the Enterprise crew's grave offense — eating in public. Successfully navigating through the tense moment, Mayweather receives the coordinates and plots a course to the creature's homeworld.
Meanwhile, Hoshi has finally made some progress on the translation. With the experimental forcefield in place, T'Pol, Hoshi, Phlox and Reed enter the cargo bay, and Hoshi attempts to communicate with the creature using the universal translator. Although she has some difficulty at first, Hoshi manages to get the message through, communicating to the creature that Enterprise will take it home. The creature releases Archer and the other crewmembers, and slowly reverts to its original size. Once Enterprise reaches the creature's homeworld, T'Pol, Hoshi, Reed and Phlox take it to the planet's surface. They are amazed to find a much larger organism, one that stretches into the horizon. As the officers look on, the creature and its severed tendril reattach to the parent organism — it is finally home.