Captain “Mal” Reynolds (Nathan Fillion), First Mate Zoe Washburn (Gina Torres), and gunman Jayne Cobb (Adam Baldwin) walk into a bar. A thug named Lund (Tom Towles) is celebrating the sixth anniversary of Unification Day with a toast. Mal, who fought as a Browncoat rebel and lost, takes it personally and picks a fight. Zoe comes to his aid, but Jayne couldn’t care less at first, but eventually joins in. They find themselves outnumbered and Mal radios his pilot “Wash” Washburn for help. Their spaceship Serenity arrives just in time. The bar patrons think it’s armed to the teeth and give up.
In the Infirmary, Doctor Simon Tam (Sean Maher) is caring for his mentally disturbed young sister River (Summer Glau), who is having nightmares about her treatment at the “Academy.” Another passenger, pastor Shepherd Book (Ron Glass), tells Mal that Simon is brave for giving up his comfortable status as a wealthy doctor to go on the run with Serenity for his sister.
On an orbiting space city—a skyplex—Mal, Zoe, and Jayne meet with the crime-lord Adelei Miska (Michael Fairman) and his huge minder Crow (Andrew Bryniarski), who shows them a bloody corpse hanging by its feet. Niska wants to hire the crew of Serenity to steal two crates from an elevated hover train between the towns of Hancock and Paradiso.
When Mal and Zoe board the train, they find an entire squad of Alliance troops aboard. After they break into the locked car and tie up the crates, Jayne is lowered on a winch from the ship above. While they are securing the cargo, a curious Fed soldier sets off Zoe’s smoke trap. In the ensuing melee, Jayne is wounded, but still manages to raise the crates to the ship’s hold. Mal knocks out the Fed, and Mal and Zoe use another smoke bomb to get back to the passenger car.
Wash parks Serenity in a canyon. Jayne says they must deliver the stolen cargo, but Wash refuses to leave his wife Zoe and his Captain Mal behind. Shepherd Book, who seems to know a lot about crime-lords for a preacher, says that if Mal is captured and could reveal to the Feds who hired him, they would all be in trouble. In Paradiso, Mal and Zoe discover they have stolen medicine needed in a poor mining town suffering an outbreak of Bowden’s Malady. The local Sheriff (Greg Henry) is suspicious of them. The ship’s other passenger, “companion” Inara (Morena Baccarin), appears and claims that Mal is her indentured servant who persuaded Zoe to leave her husband. The Sheriff, much impressed by her, lets her take them back.
On the ship, Mal announces that they will deliver the medicine to the townspeople, but Crow and his henchmen find them, and a fight ensues, which the crew of Serenity wins. The mobsters are secured, Mal and Zoe deliver the cargo to the town, but the Sheriff finds them. He lets them go. Back at Serenity, Mal offers Miska’s money to Crow, but Crow vows to hunt him down and kill him. Mal kicks Crow into the ship’s engine, and the next henchman is much more cooperative. On an Alliance cruiser, two mysterious men in suits and blue gloves (the Blue Meanies?) inquire about a girl and show the cruiser captain a picture of River Tam.
Joss Whedon and Tim Minear wrote this story in two days because Fox Studios thought the pilot, in which the characters and story were introduced, was not enough of a Western action story. In other words, it was too cerebral. The fight scene was originally written for Whedon’s Angel series. Angel’s stunt double was still in the scene. Props from Starship Troopers appear in the story. Whedon was trying to establish Mal as an anti-hero and wanted him to sell the medical cargo for the good of his crew, but the executives at Fox wanted Mal to be more likable. I’m surprised they let him toss the bad guy into the engine. Perhaps that was the deal. In any event, that was a typical Whedon surprise move.