Silent Running takes place in the not-so-distant future, at a time in which Earth's plant life has been decimated. Only a few specimens of flora have been preserved, and are currently in space in a fleet of orbiting greenhouses.
Freeman Lowell (played by Bruce Dern) is the main character, one of four extraterrestrial forest rangers aboard the Valley Forge, one of the 2,000 metre-long green house freighters. He is passionately dedicated to preserving the orbiting forests and their natural inhabitants, and eventual returning them to Earth for reforestation of his now-barren planet more so than his crewmates, whose main priority seems to be returning to Earth after their one-year deployment to space.
The main conflict comes when Lowell and his crew are ordered to destroy the orbiting greenhouses and redeploy the freighters to commercial service. Lowell decides to disobey orders and save the forests he has worked so hard to preserve.
Lowell's crewmates manage to jettison and detonate four of the six greenhouse domes on the Valley Forge. Lowell kills one of his crewmates in a struggle to save the two remaining domes, during which he seriously injures his leg. He then manages to trap the other two crewmen in the other remaining dome, which he then jettisons and destroys.
With help from the ship's three robots, Lowell feigns a premature dome detonation to fool his superiors, then alters the orbit of the Valley Forge , redirecting it towards Saturn in an attempt to preserve the last forest dome. Injured and alone with three robots, Lowell programs them to perform surgery on his leg.
Still in communication with the rest of the fleet, Lowell is informed that the Valley Forge is on a collision course with Saturn's rings, and there is nothing he can do to stop the catastrophic event. The ship will likely be destroyed. With communications failing due to the distance now between the Valley Forge and the rest of the fleet, the ship passes through the rings of Saturn. While the three robots are outside the ship on maintenance duty, one is blown away from the ship, leaving two remaining robots. The ship, and its single greenhouse dome, emerge undamaged on the other side of the rings.
Lowell and the two remaining robots chart a course into deep space, far away from the fleet. Alone except for his accompanying drones, Lowell befriends them and renames them Huey, Dewey and (posthumously) Louie. He teaches them to play poker, plant trees, and bury the killed crewmember.
Lowell soon realizes that despite all his efforts, his forest is dying from unknown causes. In a desperate and rushed attempt to save the dome he badly damages Huey in an accident with one of the ship's buggies. Repairs are unsuccessful, the forest continues dying, and Lowell begins to come to realize that his mission to save the forest is bound to fail.
After weeks alone in space, faint radio chatter is heard from a rescue party mounted from the Valley Forge's sister ship, the Berkshire, which has located the freighter after a long search. Finally able to communicate with Lowell, they inform him that they will be able to reach him within six hours he must jettison the dome but not detonate the nuclear charge, as it is too dark to do so safely.
At this point it dawns upon Lowell that what was killing the forest was lack of sunlight. With little time to work, he activates a series of lights to simulate the sun and instructs his last active robot, Dewey, to "just maintain the forest."
Realizing that his crime will be uncovered when the Berkshire finds him, Lowell jettisons the last dome to safety with the words "take good care of the forest, Dewey."
With the Berkshire only two hours away from docking, Lowell and the damaged Huey sit facing each other while he arms the last of the six nuclear charges. As he prepares to destroy himself and preserve the last dome, Lowell says to Huey: "When I was a kid, I put a note into a bottle, and it had my name and address on it. And then I threw the bottle into the ocean. And I never knew if anyone ever found it."
With that, Lowell destroys the Valley Forge with the last of the onboard nuclear charges.
The final scene is of a well-lit forest greenhouse drifting into space, tended by the sole remaining robot with a battered watering can. The scene is accompanied by Joan Baez's rendition of the film's theme song.