After discovering a new, more stable form of dilithium, Tom Paris and the rest of Voyager become convinced they can break the Warp 10 barrier. Unfortunately, simulations keep resulting in failure.
After some help by a confused Neelix, they discover a way to stabilize the problem and the planned trip is on. The shuttlecraft Cochrane is almost ready. Paris receives some negative news when the Doctor learns there is a two percent chance he would be killed. A unique medical problem affects Paris but not Kim, the other candidate to pilot the shuttle craft. Paris manages to convince Janeway, telling her he is willing to take the two percent risk.
The initial trip seems to end in failure, as Tom vanishes from sensors and communications. After a tense few minutes, his shuttle craft reappears, with Tom asleep at the controls.
Later, in Sickbay, Tom explains how he could see 'everything'. The Kazon, the Klingons, home. He explains that he knew Voyager was looking for him, so he made sure to turn off the engines. The shuttlecraft itself contains a very large amount of information about this sector of space, which would help immensely if Voyager was to break the Warp 10 barrier.
Tom doesn't feel well later, which doesn't surprise anyone. They are surprised when he falls over in the Mess Hall. It turns out he had developed an allergy...to common water. He swiftly changes, becoming unable to breathe normal oxygen.
He mutates rapidly, into an entirely new form of life. The Doctor theorizies an 'anti-proton' treatment could bring him back. During the treatment, which had to take place in Engineering, Tom escapes. He disrupts most of the systems on board and kidnaps Janeway. He steals the Cochrane and vanishes back into Transwarp.
After some time, the shuttle is located in a swamp on a planet and two amphibian beings, complete with three offspring, are found. Chakotay decides to let the offspring stay where they are. Fortunately the creatures have enough of their original human DNA left for the Doctor's treatments to work. Janeway and Paris are eventually restored back to normal.