The crew of the ship Serenity tries to evade an assassin sent to recapture one of their number who is telepathic.
In the future, a spaceship called Serenity is harboring a passenger with a deadly secret. Six rebels on the run. An assassin in puruit. When the renegade crew of Serenity agrees to hide a fugitive on their ship, they find themselves in an awesome action-packed battle between the relentless military might of a totalitarian regime who will destroy anything - or anyone - to get the girl back and the bloodthirty creatures who roam the uncharted areas of space. But, the greatest danger of all may be on their ship.
Aboard Serenity, Mal takes River along on a bank robbery against her brother's objections. They are attacked by another group of raiders: Reavers, animalistic humans who savagely eat their victims alive. They escape, but Simon decides that he and River will leave Serenity at the next port. While Mal meets fences Fanty and Mingo at a bar, a TV commercial causes River to attack the patrons with superbly effective martial arts. Before she can shoot Mal, Simon arrives and shouts a "safe word" which causes her to fall asleep. Mal carries River back to Serenity, but the incident is captured on camera. The crew contacts a reclusive hacker known as Mr. Universe who analyzes the commercial and discovers a subliminal message being broadcast across Alliance space designed to trigger River. He notes that River whispered "Miranda" before attacking.
Mal receives a call from Inara, a former passenger. Suspecting a trap but fearing she is in danger, Mal goes to her and is confronted by the Operative. The Operative offers to let Mal go free if he turns River over, but thanks to Inara's quick thinking, she and Mal escape. After another of River's outbursts, the crew discover that Miranda is a remote planet thought to have been rendered uninhabitable as the result of a terraforming accident. Serenity returns to Haven, a mining colony and home of Shepherd Book, a former passenger and friend. They discover that the outpost has been destroyed and the residents slaughtered. The Operative has ordered the deaths of all of Mal's contacts to deny him a safe haven and promises that he will continue to pursue them until he gets River.
The way to Miranda is blocked by a region swarming with Reavers, so Mal disguises Serenity as a Reaver ship. After sailing through a fleet of Reaver vessels, the crew discovers a habitable planet, but only corpses strew its cities. They discover a log recorded by an Alliance survey team explaining that the Alliance administered a chemical designed to suppress aggression in the residents, which worked too well, making them so passive they stopped working, stopped reproducing, and eventually simply laid down and died of dehydration. Instead 0.1% of the population reacted by becoming hyper-aggressive and unstable, explaining the origin of the Reavers.
Mal contacts Mr. Universe to arrange to have the log broadcast to everyone, but the Operative is already there and has Mr. Universe lure them in. Mal knows Serenity is heading into a trap, so he opens fire on one of the Reaver ships. The Reavers pursue Serenity to Mr. Universe's planet where they engage the waiting Alliance fleet. The Operative's ship is destroyed, but he survives in an escape pod. Serenity is damaged by a pursuing Reaver ship, but manages to crash land. Pilot Wash is killed by the Reavers. Finding Mr. Universe dead and his equipment wrecked, Mal learns of a secret backup transmitter from a message recorded by the dying Mr. Universe. The crew makes a stand against the Reavers to buy Mal the time to send the message. After a firefight, the crew retreat behind a set of blast doors, but the doors only partially close. Zoe and Kaylee are wounded. Simon discovers he has left his medical kit behind; as he rises to retrieve it, he is shot. He apologizes to River for failing her. She replies that it is her turn to take care of him. She charges through the opening in the blast doors, triggers the closing mechanism and throws the medical kit to Simon before the Reavers drag her away.
Mal reaches the transmitter, but The Operative is close behind. In hand-to-hand combat, Mal manages to disable his opponent and bind him to a railing, forcing him to watch the recording. Mal returns to his crew. The blast doors open to reveal that River has dispatched all of the Reavers. The wall behind her explodes, and Alliance troops rush in. The Operative, realizing he has been lied to by the government, orders his men to stand down.
After the crew erect memorials to their dead friends on Mr. Universe's moon, they patch up Serenity. Kaylee and Simon consummate their relationship. The disillusioned Operative tells Mal that the Alliance government has been weakened and that he will try his best to present his former foe in the best light, but cannot guarantee that others will not be sent after Mal and his crew. Serenity lifts off with River as Mal's new copilot.
