begins with an opening narration reminiscent of those used in the Firefly
series; when it finishes, it is revealed to be a history/politics lesson at an open-air Alliance school; a young River Tam is among the students. Though the teacher asks why the Independents fought the Unification War against the Alliance, the discussion turns to horror stories about Reavers, until River comments that the Alliance "meddles" and that people yearn for freedom.
The scene snaps to River strapped in a chair in what veteran Firefly fans know is the Academy, while scientists work on and observe her. One of them, evidently a visiting official of some sort, questions the project head about her condition and the experiments he's run. When the visitor has enough information, he triggers a device that renders the (standing) scientists unconscious, with himself (kneeling) and River (sitting) unaffected. He unstraps her from the medical equipment and chair, and tells her it's her brother, Simon, here to rescue her.
A chase ensues, but the Tams are able to duck into an air shaft and are picked up by unknown accomplices. While they are being raised to their escape, the scene freezes, and a man walks through it - the entire scene is on display as a security recording. The administrator from the recording enters, with two bodyguards, and demands the visitor's ID. He complies, and his ID marks him as an unnamed "Operative of Parliament". He lectures the administrator over the other's failure to secure River and executes him and his bodyguards by sword.
The scene cuts to the titular transport ship making a rough entry into atmo. While pilot Wash tries to land the ship in one piece, captain Malcolm Reynolds goes to survey the crew's preparations for a heist - including Jayne's absurd arsenal of weapons - and is accosted by Simon, who argues with Mal over River's role in the upcoming job. Mal vetoes the idea of leaving her, though, and the ship sets down without incident.
Mal, Jayne, Zoe, and River take their Mule (a new, hovering model after the old one was destroyed in "War Stories") into town. Mal reveals the target - a local bank is holding the payroll for a private security firm in its vaults, in hard currency. The crew enters the bank and disarms the staff, and Mal and Jayne set to work on the vaults.
River uses her telepathic skills to pick up that one of the civilians is armed, and Zoe disarms him; meanwhile Mal and Jayne find the vaults and convince the guard to surrender. While Mal and Zoe enter the vaults to gather up the cargo, though, River collapses from a telepathic read, then warns that Reavers are attacking the settlement.
The Serenity crew prepares to pull out with their cargo, while Mal instructs the vault guard to round up as many people as he can and seal them in the vault to protect against the Reavers. (Later, it's off-handedly revealed that these people are the only ones to survive the raid.) The crew pile into the Mule and depart, but not before Mal is forced to shoot a man rather than let the Reavers have him. A Reaver ship gives chase, but the crew comms ahead to Serenity
, and Wash manages to scoop them out of trouble and disable the Reaver ship in the bargain.
While the crew pulls itself together, Simon and Kaylee arrive in the hold. After ensuring his sister is safe, Simon punches Mal for putting her at risk, igniting an argument that ends with Mal evicting both of them from his ship.
lands on another colony world to finish out their deal - the payroll heist was masterminded by a criminal duo named Minto and Fanty. The two meet Mal and Jayne in the Maidenhead bar while Simon and Kaylee say a tearful farewell. However, no sooner is the deal concluded than River wanders into the bar, catching sight of the Fruity Oaty Bars commercial running on the bar's video screen. She watches, transfixed, until it ends, then whispers a single word - "Miranda" - and proceeds the punch the nearest patron unconscious.
As the bar brawl spreads, River holding her own against all comers, Jayne and Mal take notice. Jayne goes to subdue River normally and is knocked out for his trouble, while Mal rushes to get his pistol out of lockup. River takes a pistol from one of her opponents and she and Mal aim at the same moment, when Simon arrives and utters a phrase that causes River to fall unconscious.
Back on Serenity
, River is imprisoned in a makeshift cell while Simon tries to explain what he knows of her training and the safe code he used. Mal is unwilling to simply abandon the two fugitives, and Wash suggests they ask an old friend, Mr. Universe, a hacker and tech junkie who set up shop on an out-of-the-way planetoid and monitors all transmissions in the system. Mr. Universe is able to identify a subliminal message hidden in the Fruity Oaty Bars commercial as a military encrypt, recently broadcast over and over again in an attempt to find her. Simon tends to River and attempts to coax the meaning of "Miranda" from her, but is unsuccessful.
A brief scene features the previously-absent Inara welcoming the Operative to her new lodgings, wherever they are. However, she seems to recognize straight away that he's up to no good.
Lacking better options, Mal takes the Serenity
, including the Tams, to the Haven colony, home of their former passenger, Shepherd Book. Book greets them and offers them the hospitality of the colony, while discussing strategy with Mal. He displays incredible knowledge of Operatives and Alliance workings, hinting that he had previous jobs before becoming a Shepherd.
A dream sequence begins, in the school/park with young River and the teacher from the prologue. The teacher instructs the class to lie down; they comply, except for River. She refuses until a vision of a set of prone, desiccated corpses comes, and she wakes.
In his own quarters, Mal is awakened by a wave from Inara, who is unusually courteous, suggesting that the local Companion house is having local trouble and would appreciate the Serenity crew around as support. He notices her strange behaviors and deduces that she's trying to warn him of a trap. The crew, who has been listening in, need little convincing, but rather than running, Mal intends to pull Inara out of the trap, by force if necessary.
Mal sneaks into the Companion house and meets with Inara, who is shocked he even came. Their conversation is interrupted by the Operative, who attempts to convince Mal to turn over River and Simon. Inara takes out a stick of incense, claiming she's praying for Mal, and Mal predictably turns down his offer. The Operative threatens to destroy Serenity
by locking onto its pulse beacon - and Mal counters by revealing he brought the device with him. The Operative engages Mal and Inara in hand-to-hand combat, with the Operative eventually defeating them and retrieving his sword. However, Inara's "incense" - actually a flashbang grenade - detonates before he can make the kill, stunning the Operative and allowing Mal and Inara to escape. Serenity
sows a set of bogus navigational sensors to confuse trackers and breaks for Haven.
The crew debate their options while en route, but come to no real conclusions, and head off to sleep.
River dreams again of the schoolhouse - but this time, the schoolhouse is deserted except for the adult River, dressed in her Academy smock. She stares at the display on her desk - a navigational view of a planet - until the visions of corpses come again, followed by a Reaver that shocks her awake.
In the mess, Jayne is awake, having a drink, when he decides to take matters into his own hands concerning River. He enters her cell, but is knocked out, alerting the rest of the crew. They split up to find her, but are under orders not to fight. She finds and disables Simon, then makes her way to the bridge. Mal sneaks onto the bridge behind her - she offhandedly holds him at gunpoint while working the navigation console. Mal tries to talk her down, but she ignores his, working the console until she declares "Miranda". The nav display shows the planet from her dream.
The crew crowds around the display, studying the display on Miranda. Evidently it's a black rock, uninhabitable, but there's no record of it on the Cortex. Mal guesses that the Alliance is trying to keep a planet-sized secret buried - unfortunately, the way to Miranda lies through Reaver-infested space.
Swinging into view of Haven, the crew finds the town burned by unknown hands - but the cause is easy to guess. A dying Book confirms the Alliance razed the town - but the lack of ambush means the Alliance was shooting blankly at old Serenity
haunts. The Operative waves Mal to confirm the destruction of the various safeholds and repeat his offer to turn over River, stating his goal of creating a "world without sin".
Mal devises a new, desperate plan. Using bodies, bits of wreckage, and a little ingenuity, he intends to transform Serenity
into a facsimile Reaver ship and reach Miranda. He browbeats the crew into aiding him, Serenity
sets off on its dangerous trek, aided by a new disguise and a salvaged anti-air cannon.
The crew, especially River, looks on in horror at the Reaver fleet, but Serenity
is able to pass through unchallenged. They reach Miranda and find it deserted, but a picturesque, successfully terraformed world. Picking up a weak beacon, they land and enter a city, completely free of people. They find a few corpses, decayed but not showing any signs of violent death - indeed, any signs of what could have possibly killed them. River is overcome by more visions of bodies and a feeling of thousands of voices "saying nothing" in her mind.
They find the beacon in a search-and-rescue base, and are able to reactivate some of its systems. A little investigation and they find a holographic recording of a scientist, recording the aftereffects of a disaster - no terraforming blip, though... no natural disaster or disease. The scientist blames it on a substance called "Pax" added by the Alliance to the atmosphere processors. According to her report, it was intended to calm the population, but worked too well
, sending people into a deep lethargy. However, about a tenth of a percent had an extreme reaction and grew more
violent... and became the Reavers.
Safely aboard Serenity
, Mal addresses the crew. He lays out his new plan: reach Mr. Universe so he can rebroadcast the Miranda recording throughout Alliance space. However, as Wash points out, they'll have to contend with Reavers and
the Operative's fleet - and it's likely the Alliance knows about Mr. Universe.
And, in fact, the Operative is paying Mr. Universe a visit as they call; as soon as the crew is off the line, the Operative kills Mr. Universe and orders his equipment destroyed, and a fleet assembled to capture or destroy Serenity
, meanwhile, fords most of the Reaver fleet without incident... but engages and destroys a Reaver picket on the far fringe, prompting the entire
fleet ot give chase. When they arrive in the ion cloud, the Operative is waiting - but the Reaver ships catch him by surprise. Serenity
slips through the chaos as Alliance and Reaver ships proceed with blowing each other out of space. The Operative's cruiser is destroyed, but he manages to escape in a pod and land on the surface.
However, a Reaver ship catches the Serenity
in low atmosphere, disabling their engines and forcing them to make a hard landing, with Reavers hot on their tail. Wash manages to land the ship more or less intact, only to be killed by a Reaver harpoon moments later. The rest of the crew debarks safely, carrying the Miranda recording and all the weapons they can find.
Zoe and the crew set up a chokepoint to defend while Mal heads into the underlevels to transmit the message. They set up a wall of crates, ready their weapons... and wait.
In the underlevel, Mal finds Mr. Universe's setup ruined - but a message, recorded by his lovebot as he died, tells Mal of a hidden backup transmitter, just above the power core. He hurries down, desperate now.
On the line, as the crew checks their weapons the last time, River collapses from the rage of the Reavers... and Simon and Kaylee admit to their feelings as the Reavers pound the doors open.
The Operative finds a hidden route into Mr. Universe's sanctuary and hears the recorded message about the backup and sets off to stop Mal. He and Mal end up fighting atop a giant open set of girders over the power generators.
Meanwhile, Zoe breaks the line, eager for revenge against the Reavers, but is injured in the process. The others manage to hold for the moment... but the Reavers begin breaking through the walls of the chokepoint, and disable Kaylee with an attack. Zoe orders a fallback to the heavy blast doors. Simon realizes in desperation that he left his medkit on the line, tries to retrieve it, and is shot. While Inara tries to tend to him, Jayne fends off the Reavers solo. River finally snaps out of her terrified state, declares it's her turn to take care of them all, and vaults through the door. She tosses back the medkit and seals the door...
Neither Mal nor the Operative have gained the upper hand... until the Operative draws and stabs Mal with his sword. Mal, however, headbutts him, pulls out the sword, and continues the fight. The Operative tries to disable Mal with the nerve strike he used earlier - only for Mal to reveal that the nerves in question had been removed due to war injuries. Mal pins the Operative to a safety railing using his own sword and the straps on his uniform - and spares him, offering to "grant his greatest wish" and show him the world without sin. Mal accesses the communications equipment and sets to broadwave the Miranda recording, before heading to the exit.
River, trapped in a room with an unknown number of Reavers - proceeds to annihilate them all. As graceful and deadly as in the Maidenhead again, she clears the entire room
as Mal exits the lift. Just as he asks what happened to River, the blast doors open, revealing her unscathed in a room full of Reaver corpses. An Alliance contingent enters the room, calling for her to stand down, and she prepares to fight them, as well... but the Operative orders them to stand down, realizing the damage is done.
A funeral is held on Haven for Shepherd Book, Wash, and Mr. Universe, with the surviving Serenity crew in attendance. Then they proceed with the more hopeful task of rebuilding Serenity
- replacing lost parts, removing the fake signs of Reaver ownership, even repainting the ship's sigil. Simon and Kaylee even find some private time in the works. The ship finally receives its green light, and though the Operative warns that Parliament is not forgiving, Mal is confident they'll be able to make it.
Tropes used in this movie include: