After researching the Moneans' predicament, Janeway tells Burkus the ocean will suffer a complete loss of containment in less than five years. Meanwhile, deep beneath the ocean's surface, the shuttle crew encounters an ancient field reactor controlled by a core computer. As they upload information from it, the Delta Flyer is attacked by an enormous marine creature discharging an electrical current. It retreats when hit by a phaser, but the shuttle has already been breached, and water begins pouring into the cabin.

Once the leak is repaired, the shuttle crew determines the reactor core is unstable, so Paris initiates a power transfer as a temporary solution. Reviewing the uploaded information, he finds the ocean was once part of a landmass inhabited by a very advanced civilization. They used a kinetic transfer system to draw the water around the reactor, but it is not responsible for the containment loss. Instead, Paris determines it is the Moneans' mining operation that is destroying the ocean.

Janeway offers Burkus several solutions that would make the refineries obsolete, but he only plans to include them in a subcommittee report. Paris is distraught over the ocean's destruction and feels Burkus doesn't understand the magnitude of the crisis. Forbidden to disrupt the internal affairs of an alien race, Paris instead convinces Riga to take the oxygen refineries off-line, and the two commandeer the Delta Flyer.

Janeway immediately orders Paris to cease his mission. When he refuses, she prepares to modify a photon torpedo as a "depth charge" to stop him. Once they reach the reactor, Paris and Riga launch their missile at the same time Voyager fires. Paris' missile is deflected, and he is brought back to the ship and reduced to the rank of ensign. Once he finishes the letter to his father, he files it in his personal log to be sent when Voyager is within Earth's range.