Part 1 In 2511, a squad of "Independents", led by
Sergeant Malcolm "Mal" Reynolds and
Corporal Zoe Alleyne, fight in the Battle of Serenity Valley during the Unification War. Despite Mal's insistence that the battle can be won with air support, Zoe receives orders to surrender from the leaders of the rebellion. Mal is forced to watch in horror as
Alliance ships sweep the battlefield unopposed, destroying the rest of the Independents. Six years later, Mal is the captain of his own transport ship, an older-model
Firefly-class vessel he named
Serenity, with Zoe as his second-in-command. The rest of the ship's crew consists of
Wash (
Alan Tudyk), who is the pilot and Zoe's husband;
Kaylee (
Jewel Staite), the engineer; and
Jayne Cobb (
Adam Baldwin), an untrustworthy gun-for-hire.
Inara (
Morena Baccarin), a "
Companion" (a very high-class
courtesan) who rents one of
Serenitys two shuttles, normally travels with them, but she is currently away on business. While the crew are illegally salvaging some crates off a derelict Alliance spaceship, they are spotted by an Alliance cruiser. To escape capture, Mal has Wash deploy a fake distress beacon. The Alliance cruiser falls for the deception, but broadcasts a bulletin that a
Firefly-class ship is carrying stolen Alliance goods. The crew of
Serenity travel to Persephone to deliver the stolen goods to
Badger (
Mark Sheppard), the small-time crime lord who hired them for the heist. However, Badger reneges on their deal after learning that the Alliance has put a bulletin on Mal's crew. He also does not like the way Mal looks down on him. Mal decides to try selling the cargo to
Patience, an old business associate who lives on Whitefall. Zoe has misgivings, since Patience shot Mal the last time they met, but Mal is desperate to get rid of the hot cargo. The crew picks up passengers before leaving Persephone for extra income, and Inara rejoins the ship. The new passengers are a
preacher named
Shepherd Book (
Ron Glass), a bumbling man named
Dobson (
Carlos Jacott), and a wealthy doctor named
Simon Tam (
Sean Maher) who brings aboard a mysterious large crate. En route to Whitefall, Wash discovers that someone on board sent a message hailing the nearest Alliance cruiser. Suspecting that Simon is the mole, Mal confronts him, only to discover that Dobson is actually an undercover Alliance lawman. Dobson surprises Mal by telling them it's Simon he wants to arrest, not Mal. During the tense confrontation, a nervous Dobson accidentally shoots Kaylee in the stomach before being overpowered by Book, who manages to easily disarm and subdue him. When an Alliance cruiser orders them to dock for prisoner transfer, Simon threatens not to treat Kaylee if they do not flee. Mal reluctantly agrees (after being prodded by Inara to do so), but then has Jayne restrain Simon while he opens Simon's mysterious crate, only to be surprised to find a naked young woman inside in
cryonic sleep.
Part 2 The woman in the crate is
River Tam (
Summer Glau), Simon's younger sister. Simon explains that his sister was a brilliant child prodigy who was sent to an elite, but secretive Alliance academy when she was fourteen. After River sent him an encoded letter for help, he discovered that the Alliance was experimenting on the academy students. Simon abandoned his career as a successful trauma surgeon to rescue her and spent all of his money to get her smuggled out of the academy. The Alliance wants River back very badly. Mal decides to proceed to Whitefall as planned and drop off both the goods and the Tam siblings. Mal tells Jayne to interrogate Dobson to find out what he told the Alliance about them. Once Jayne finds out that the Alliance knows nothing, Dobson tries to bribe him, offering him enough money to buy his own ship. Soon after, they discover that a
Reaver ship is approaching. Zoe explains to Simon that "If they take the ship, they'll rape us to death, eat our flesh and sew our skins into their clothing. And if we're very very lucky, they'll do it in that order." Luckily, the Reaver ship passes by without incident.
Serenity lands on Whitefall. Not trusting Patience, Mal sends Jayne to take out her hidden
sniper while he and Zoe meet Patience and some of her henchmen in a barren valley. Mal gives Patience a sample of the cargo ("Genuine A grade foodstuffs...
protein,
vitamins...
immunization supplements" that looks like a
chocolate). As expected, Patience tries to kill them after learning where they have buried the rest, but Mal, Zoe and Jayne gun down Patience's men. Mal leaves Patience alive, but takes the money he was promised. Jayne is warned by Wash that the Reavers turned around and followed them to Whitefall. Meanwhile, back on the ship Dobson escapes, knocking out Book and grabbing River. Mal returns and calmly shoots Dobson in the head, dumping his body off the ship as they start to lift off, the Reavers hot on their tail. Mal orders Inara, Book, Simon and River to go to Inara's shuttle, just in case the ship is boarded. Jayne carries the still-convalescing Kaylee to the engine room, and Book offers to help her. With Jayne and Book carrying out Kaylee's instructions, Wash is able to pull off a "
Crazy Ivan" (
VIFF), and
Serenity manages to shake the pursuing Reavers. Jayne tells Mal that they should dump the siblings since Dobson had told him that the Alliance will keep coming after River. Mal asks Jayne why he did not turn against him. Jayne responds that the money Dobson offered was not enough. Mal suggests to Simon that he and River might be safer on the move, and points out that
Serenity is always moving, and in need of a qualified ship's
medic. Simon reluctantly accepts his offer. == Deleted scenes ==