"On this first day of a new century we humbly beg forgiveness and dedicate these last forests of our once beautiful nation to the hope that they will one day return and grace our foul earth. Until that day may God bless these gardens and the brave men who care for them."
--United States President, Anderson

The Valley Forge is one of three cargo vessels (Valley Forge, Sequoia, and Berkshire) orbiting our sun near Saturn. Each ship carries six domes housing biospheres, representing what is left of our Earth's biomes. They are ordered to abandon and nuclear destruct all the forests and return ships to commercial services. No explanation is given. Freeman Lowell finds the decision "insane", kills the other three crew members (John Keenan, Marty Barker, and Andy Wolf) and manages to stop them from destroying the last dome. Lowell recognizes that having killed his crew mates and harboring the last dome does not fit company orders. As the ships enters a communications blackout, he decides to break formation, feigning damage. The ship's maintenance drones are instructed to dump cargo overboard simulating ship damage, an old submarine trick called "Silent Running".

The ship passes through the North Eastern quadrant of Saturn's rings sustaining minor damage, though losing one drone. Lowell spends time with the forests and personalizes the drones, giving them names. The forest starts to die and Freeman searches for a cure. After some time the ship emerges from behind Saturn and is contacted by the other ships. Freeman is told to jettison the last dome, but not blow it up because "it's awfully dark out here". He realizes the lack of sunlight was the forest's health problem, and sets up lights in the dome. Freeman programs Dewey, the last functioning drone, to care for the forest and launches it into space perhaps to be retrieved some day, a "message in a bottle" for a future time. Since Lowell cannot come to terms with a human race that condones such waste (or the fact he killed his mates), he decides to detonate the remaining bombs, destroying himself along with the Valley Forge.