Captain Malcolm "Mal" Reynolds, his first mate, Zoe, and fellow crewman Jayne Cobb are in a bar. When Lund, one of the other bar patrons gives a loud drunken toast celebrating the anniversary of Unification Day, former Browncoat rebel Mal picks a fight. Zoe, who fought with Mal in the war, immediately steps up to help him. Tough-guy Jayne holds back at first ("Hey, I didn't fight in no war. Best of luck, though."), but eventually joins the fight just for the fun of it. As the entire bar attacks them, Mal radios his pilot, Wash, who also happens to be Zoe's husband, and shortly Serenity dramatically backs up the hapless crew.
Mal runs into one of the passengers in the ship's infirmary, Dr. Simon Tam. Simon is tending to his mentally-disturbed teenage sister River, who occasionally shows flashes of her old genius hidden beneath her insanity. Outside the infirmary, Mal sees one of the other passengers, Book, a "shepherd" (preacher). Book tells Mal that Simon is very brave for giving up his life as a wealthy doctor to go on the run from the Alliance in order to protect his sister. Book senses that while Mal pretends to be merely an unsympathetic Smuggler, he is protecting the fugitives out of a sense of honor, despite the risk of drawing attention from the Alliance. Mal finds Inara Serra brushing Kaylee Frye's hair in Inara's shuttle. Inara is a beautiful Companion, a licensed and well-respected courtesan, and Kaylee is the ship's mechanic. The local crime lord, Adelei Niska hires the ship for their next smuggling job.
On a "skyplex" (an orbiting space city), Mal, Zoe, and Jayne meet with Niska and his giant brutish lieutenant Crow. In order to cement his reputation, and show that he is serious, Niska shows them a bloody dead body hanging by his feet. He killed this man (his wife's nephew), for failing to do a job. Niska outlines the job for Mal and his crew - steal two crates of an unnamed Alliance cargo from a train as it travels from Hancock to Paradiso, and deliver it to Crow at the rendezvous point.
When Mal and Zoe board the train, they discover that an "entire squad" of Alliance troops are also aboard - though not specifically guarding the cargo. After they break into the locked train car and secure the crates, Jayne is lowered in on a winch while Serenity hovers over the train. While they attach the cargo to the winch, a curious Fed trips a smoke trap at the car door. In the resulting melee, a wounded Jayne is hoisted back to the ship, Mal knocks out the Fed before he sees what's happening, and Mal and Zoe use the smoke as cover to re-enter the passenger car.
On Serenity, Simon patches up Jayne's leg and gives him a shot while Wash parks the ship in a canyon near Paradiso - NOT the rendezvous point. Jayne tells the crew that they should finish the job, leave Mal and Zoe behind, and deliver the cargo to the dangerous Niska. Wash won't leave without his wife and the captain. Shepherd Book, who knows a lot about crime lords for a Shepherd, states that, "If Niska finds out [Mal] is being held, and may speak as to who hired him - I think we're better off being a little late."
Meanwhile, in Paradiso, Mal and Zoe are aghast to find that the cargo was critical medicine for this poor mining town, in which everyone is suffering from "Bowden's malady," a degenerative disease. The local sheriff, who is questioning everyone from the train, is suspicious of Mal's cover story. Inara appears, and the working-class townspeople, who have never seen a Companion before, make a big fuss over her. Inara plays up her respectable status as a Companion, claiming that Mal is her runaway "indentured man" who persuaded Zoe to leave her husband and escape with him. She tells the Sheriff that she is taking the "runaways" back into her own custody.
Back on the ship, Mal announces to the crew that they will be returning the cargo to the townspeople. However, Crow arrives with henchmen and a violent fight ensues, which the Serenity crew wins. After the villains are secured, Mal and Zoe drive the cargo back to town. They intend to drop off the crates and notify the sheriff once they're well away, but they run into the Sheriff who has overheard their conversation. Realizing the cargo is intact, the sheriff decides to let them go, respecting their courage to do the right thing.
Outside Serenity, Mal returns Niska's money to a trussed-up Crow, proposing that they will stay out of Niska's way from then on. When Crow rejects the offer and threatens to hunt him down wherever he goes, Mal casually kicks him into Serenity's engine intake. Another trussed-up henchman is then brought before Mal — who begins repeating his proposal — but the second man quickly agrees to take the money back to Niska.
Back on the Alliance cruiser, two mysterious men in suits and wearing blue gloves inquire about a girl — and show the captain a photo of River Tam.
Reproduced from Wikipedia under the Creative Commons Attribution-ShareAlike License.
Simon: River? River, it's okay. It's me. You know who I am?