The pre-title teaser serves to bring those unfamiliar with the Firefly TV series up to speed with the movie's timeline. The events in the teaser occur prior to the first episode of the TV series.

The Universal logo changes to show ships leaving 25th Century Earth as the teacher's voiceover describes the exodus from "Earth that was" and the terraforming and colonization of the new 'verse'.

An introduction to the system government known as the Alliance follows, mentioning the war for system-wide control -- the War of Independence for the losing opposition, the Browncoats. This classroom scenario is seen to be the dream of River Tam (Summer Glau), who is in a drugged sleep under confinement at the Alliance Academy facility, being groomed as some form of programmed assassin. We see River's brother, Dr. Simon Tam (Sean Maher), infiltrate the lab and free her; then we see the breakout was a security recording viewed after the event by the Operative (Chiwetel Ejiofor). He has orders to deal with the security lapse and the project director's failure as well as to find and ensure River's return.

The credit sequence, set eight months after the events of the teaser, introduces us to the "Firefly" class freighter Serenity, owned and captained by former Independent soldier Malcolm (Mal) Reynolds (Nathan Fillion). Serenity is about to break atmo on the planet Lilac on one of the crews' not-always-legal jobs -- this time a bank heist. The crew members are familiar to Firefly fans, but for newcomers, their positions on the boat help introduce them. The pilot, Hoban "Wash" Washburn (Alan Tudyk), is married to the second in command, Zoe (Gina Torres), a veteran and war comrade of Mal's. We meet the hired gun, Jayne Cobb (Adam Baldwin), and the engineer, Kaywinnet Lee "KayLee" Frye (Jewel Staite) going about their jobs.

Two faces familiar from the series are no longer aboard, but we meet them later: the "companion," Inara Serra (Morena Baccarin), and a shepherd (preacher), Derria Book (Ron Glass). (For information on why Inara and Book left the ship, see IMDB discussion boards.)

After River's escape, the Tams found sanctuary with this crew, but this is under protest as Mal plans to make use of River's psychic abilities on this job -- against Simon's wishes. It begins without any major hitch, then River senses and warns them of arriving of Reavers. On the border planets, Reavers are feared for their unprovoked, cannibalistic, frenzied attacks; they are only known from urban legend to most on central planets.

The crew has an eventful escape, Mal shooting a man who wanted to escape rather than letting him be captured by the Reavers. Back aboard in relative safety, Simon punches Mal for endangering River, then declares their intention to leave the ship. Kaylee, with her crush on Simon, is distressed.

Fanty and Mingo (the Feldman twins), Mal's sponsors for the job, are waiting for them at the Maidenhead Bar on Beaumonde, and want more of the take. River enters the bar and sees an ad on the viewscreen. This triggers her combat training; she whispers 'Miranda' and begins systematically taking out everyone around her. The twins run. Jayne tries to stop River and fails, while Mal gets to his gun and aims at the exact moment River aims a captured weapon back at him.

Simon enters, sending her to sleep with a code word he knows. Mal brings them back aboard Serenity. Meanwhile the Operative, who ordered the broadcast of the trigger to expose River, is viewing the bar's security feed on his command ship, and a profile of Mal.

Wash suggests a talk with Mr. Universe (David Krumholtz), a kind of media hacker with knowledge of all kinds, who lives with his 'Lovebot' on his own moon. He tells the crew the advert code triggering River's combat training was high level Alliance military. There is something they want and River is part. We then see Inara greet the Operative arriving at the temple where she's living now; with her intuition and training, she realizes something is wrong.

Meanwhile, the crew arrives at Haven, the mining colony where Shepherd Book now has a congregation and are greeted by him. Book has unusual knowledge of security, criminal and military activity, which puzzles Mal, no explanation ever given. Book advises Mal on how an attack by an Operative against him could occur. Referring to Book's past, Mal says "You have to tell me about it sometime." Book replies, "No...I don't."

Inara makes contact with Serenity, asking for help. Mal, sensing a trap ("You saw us fight? No? -- Trap!"), decides to go see her. The Operative is at the temple -- of course it was a trap -- and he outlines the trouble River will bring Mal, trying to get him to hand River over. Mal shoots him, then fights him. Inara sets off a flash bomb, and they escape in the nearby shuttle while Serenity deploys decoys to throw the Operative off the trail.

Jayne, after arguing with Mal about keeping River, tries to take her from the locker she's held in. Overpowering him, she escapes. On the bridge, she shows Mal the planet Miranda. Miranda's existence has been suppressed -- all mention of it deleted from records -- and it's in the region known to be Reaver territory.

The Alliance gets to Haven before the crew returns, destroying the settlement. They find Book, dying, beside the settlement's cannon, which he used to shoot down the attacking craft. His last words tell Mal to have strength in his beliefs. They realize the Operative attacked all places Mal could have gone, cutting off escape. Mal finds another way; they disguise Serenity as a Reaver ship and make their way to Miranda, passing through a Reaver flotilla. Their disguise successful, they find a planet apparently suitable for life with breathable air, power, intact cities and infrastructure. But all the people are dead. The inhabitants appear to have simply lost the will to live and laid down to die: at work, on the road, in their houses.They find a survey ship with a holographic recording from its last surviving team member, a report never sent. The recording reveals the Alliance put chemicals into the air processors on Miranda to stabilize the population's behavior. It worked too well. Almost everyone stopped doing anything to live and died. A fractional percentage, however, had a drastically different response to the chemical: they became insanely violent and aggressive. The crew realizes this damaged and dangerous remnant of Miranda's inhabitants are the Reavers. The Alliance created them and tried to bury the evidence just before the War. This knowledge affected River, and the release of the tension in her makes her throw up. She says lucidly "I'm all right" after this. River apparently picked up the memory from some of the Alliance chiefs who came to see her training and the memory was also triggered by the code advert. Mal decides to broadcast the hologram from the place Mr. Universe is.

Mal calls Mr. Universe, who says come ahead. But he's already held prisoner, and as soon as Mal breaks contact, he's killed by the Operative. As they pass back through the Reaver flotilla, Mal mans the Haven cannon they took for the ship's disguise. He blasts one of the Reaver ships and Serenity runs for it, Reavers in hot pursuit. The Operative's fleet is concealed in the atmospheric ion cloud of Mr. Universe's moon, and they're surprised when Serenity comes right at the command ship. They're even more surprised by the many Reavers on Serenity's tail. Wash expertly slips Serenity through the ensuing battle, covered by the confusion, until they get tagged by an electronic pulse weapon that takes out Serenity's electrical systems. Wash manages a dead stick crash landing, skidding into an open hangar bay at the end of the runway. Serenity loses one of its attitude engines, turning 180 degrees facing out of the hangar as it comes to rest, leaving them open to attack by the Reaver ship following them in. A spear weapon breaks the window, impaling Wash. He dies not long afterwards. Zoe tries to free him, but Mal sees another spear launched and gets Zoe out of range. They and everone else get inside Mr. Universe's complex. Jayne and Zoe arrange a defensive strategy, while Mal goes to broadcast the message. He finds Mr. Universe dead, but the Lovebot activates at Mal's approach, delivering Mr. Universe's last message on how to find a hidden transmitter the Alliance would have missed when destroying his equipment.

The Operative, having escaped his ship's destruction in a lifepod, arrives shortly afterwards and also triggers the Lovebot message intended for Mal; he follows Mal to the transmitter. On the hangar level, Reavers attack. Zoe gets slashed in the back taking close combat revenge. Kaylee gets hit, and Simon, realizing his medical bag was left behind out where the Reavers are, stands up looking for it and also gets hit. He apologizes to River for leaving. She says "You always take care of me...My turn." She dives through a gap in the blast door they were defending; throws Simon's bag back, grabs a fallen weapon and fights with it before closing the door's manual override and being grabbed by Reavers.

Mal gets to the transmitter, has a massive fight with the Operative and manages to beat him this time, letting him live then setting him to watch the evidence while Mal broadcasts it.

River's fight continues, with her training ensuring she stands up. Mal returns to the group as power returns to the complex and they're wondering whether River survived. The blast door reopens, revealing her standing alone with bladed weapons in her hands as the wall is demolished. Alliance troops storm in demanding "Weapons down;" they request a kill order from the Operative. He tells them to lower weapons. "We're finished."

We next see the funeral service for the fallen crew members. There are memorials for Wash, Book, and Mr. Universe. Rebuilding work on Serenity comes next; we see Kaylee and Simon kissing, observed from above by River. Before he leaves, the Operative comes to tell Mal he has weakened the Alliance, but they're not gone, and not forgiving. Mal meets Inara aboard as they prepare to leave, asking if she's ready to get back to civilized life. She's not sure. "Good answer," he says. River is in the co-pilot seat as Mal goes to the pilot chair; she seems to know what she's doing and lifts the ship before Mal quite realizes what she's up to. He tells her how important it is to love your ship. A panel tears loose from the hull as Serenity disappears into the black sky. Mal, voice-over, in an urgent tone: "What was that?"