While making a pit stop at an interstellar truck stop, Fry buys and eats an extremely old egg salad sandwich from a vending machine in the restroom. On returning to Earth, Fry and Bender are assigned the task of fixing the plasma fusion boiler, which promptly explodes. Bender is not damaged, but Fry is impaled by a large pipe. Despite the severity of the injury, Fry's damaged body repairs itself in seconds, and the subsequent medical examination reveals to the crew that Fry is infested with microscopic worms from the egg salad.
To eliminate the infestation, Professor Farnsworth makes miniature robotic versions of the crew, except for Fry and Leela. Because the worms know all that Fry knows and would thus defend themselves if Fry knew about the mission, Leela is assigned to distract Fry, who is not told what is happening. Controlling the micro-droids using virtual reality gear — which is apparently cheaper than actually shrinking the crew themselves — the crew board a miniature Planet Express ship, and enter Fry's ear. Throughout the travel, the crew discover that the worms are drastically improving Fry's intelligence, health and fitness.
The crew make their way into Fry's bowel, and fight their way to the pelvic splanchnic ganglion, intending to cause a massive bowel movement to expel the worm society (or, as the Professor puts it, "Listen, this is gonna be one hell of a bowel movement; afterwards, he'll be lucky to have any bones left"). Meanwhile, Leela is enchanted by the now intelligent and muscular Fry. He then reveals that he loves her but only recently was he able to articulate his thoughts. She realizes that the worms are responsible for the new, improved Fry, and sets out to stop the Professor. Her micro-droid reaches the nerve, and hacks the rest of the micro-droid crew to pieces with an axe. The Professor tells her that the worms will burrow so deep into Fry's body, he will be stuck with them forever, but Leela reasons that Fry is better off with the worms.
Fry is informed of what has been happening, but is more interested in romancing Leela than clearing the worms out of his body. Although the two share a romantic evening at Leela's apartment — made more powerful when Fry composes Leela a sonnet on the complex musical instrument the Holophonor — Leela tells Fry that she loves the new him. Worried, Fry tells her that he needs to find out something, leaves and, using his own micro-droid, enters his own body.
Fry confronts the worm leader and engages him in a swordfight after asking the worms to leave so he can learn if Leela loves him or just what they have made of him; he eventually blackmails the worms into leaving by threatening to kill himself by destroying the medulla oblongata, and they comply. With the worms gone, Fry returns to Leela's apartment, intent on finding out if Leela can love him as he truly is. Fry explains to Leela about the worms, and his decision to dispose of them. His awkward attempts at being romantic end when he mentions his previous relationship with Amy, and Leela kicks him out of her apartment. Back at his apartment, Fry begins to re-learn the Holophonor, and creates a crude image of Leela.