1The Train Job
Mal and his crew are recruited by a greedy and sadistic gangster, named Niska, to pull off an old-fashioned train robbery. Although the heist goes off without a hitch, Mal and Zoe are detained by the authorities only then to learn that the cargo they stole was medicine going to refugees and are torn whether to risk giving back the cargo and not getting payed for the job.
The crew of Serenity stumble upon the ruins of a transport ship and decide to search the vessel for any salvageable goods, only to discover that the ship is not entirely deserted.
3Our Mrs. Reynolds
A woman claiming to be Mal's wife appears aboard Serenity. Everyone is shocked by Mal's new wife, Saffron, and reacts differently for Jayne is jealous, Inara is outraged, Kaylee is happy for Mal, while Zoe, Wash, Book, Simon and River don't know what to think. But the good-natured, young Saffron is soon revealed to be not all as she appears.
The crew pulls a heist in a town where Jayne once robbed the local magistrate, making him a local folk hero, and a target for the local police.
5Out of Gas
On Simon's birthday, Serenity's engine stops turning and an explosion knocks out auxiliary life support, severely wounding Zoe. With few options, Mal orders the rest of the crew off the ship, but he stays behind hoping for a miracle. The story is told in multiple time frames shifting from Mal's time alone on the ship to the events prior to the crew's departure. Flashbacks to Mal's initial meetings with many of his crew members are also a part of the narrative, showing how and why Mal and Zoe decided to buy the old Firefly-class ship, as well as revealing it wasn't love-at-first-sight for Zoe and Wash when he was hired as the Serenity's pilot, as well as how Inara charmed her way into letting Mal rent out one of the Serenity's shuttles for herself, how Mal met the mechanic/engineer Kaylee in a compromising position, and how the crew met Jayne who was an tough, but dumb, interplanetary bandit.
While pursuing a smuggling job, Mal and Kaylee go undercover at an upper class fancy dress ball. Inara is attending the same ball with her wealthy client, Atherton Wing. In an attempt to defend Inara's honor after Atheron makes an offensive comment, Mal punches Atherton in the face. Outraged, Atherton challenges Mal to an old-fashioned duel using swords. Meanwhile, Badger returns and under Atherton's payroll, holds the Serenity crew hostage, while River begins showing some more of her sane side in a verbal confrontation.
While visiting an outlying planet, Simon and River are kidnapped by local villagers in need of a doctor. Meanwhile, the rest of the crew are forced to seek medical help from an unlikely source when one of their own is shot.
When the crew of Serenity arrives on the heavily populated, industrialized Alliance core world of 'Ariel', where Inara is to undergo an annual physical examination for her clean companion medical record, Simon realizes it is the perfect opportunity to sneak River into an Alliance medical facility and find out what they did to her. In return for the crew's help in getting them in to the facility, Simon helps Mal, Zoe and Jayne organize an operation to steal valuable medical supplies. But Jayne has other ideas when he learns about the reward for Simon and River and contacts the local authorities, leading to another appearance of the two, sinister-looking, 'blue-gloved agents'.
Wash begins to feel threatened by the bond between Mal and Zoe. In order to see for himself how the two work together, Wash demands that he goes on a mission with Mal to sell the stolen Ariel medical supplies instead of Zoe. Unfortunately, the ruthless and sadistic gangster Niska has found out where the Serenity is and captures Mal and Wash and tortures them as revenge for their failure in the train robbery mission (from The Train Job episode). Meanwhile, Inara has another client whom is a wealthy counsel person on the planet they're on and to the crew's surprise, the client is a woman. When Zoe learns about Niska's abduction of Wash and Mal, she tries to strike a bargain for their release, but Niska steals all their money and stolen cargo, while releasing only Wash. Wash realizes that Mal was willing to sacrifice himself for Wash, he persuades Zoe, Jayne and Book and the rest of the crew to help him launch a rescue mission in a full-scale attack on Niska's fortified space station to save Mal. Also, River begins showing more developing powers when she displays some accurate 'blind-shooting' during the rescue when Kaylee is pinned down during the climatic gun battle.
10Objects in Space
The Alliance has placed a bounty on River Tam's head and a bounty Hunter named Jubal Early sets out to claim the bounty and tracks down the Serenity crew. Jubal sneaks on-board the Serenity while the crew is asleep to capture River and Simon and return them to the Alliance, so he can be paid for their capture and only River can stop him.
In the first half of the original pilot episode, the crew of Serenity takes on several passengers and make their way to another planet to try and sell goods they salvaged from a wrecked ship. Their efforts are impeded, though, when Wash and Mal realize that there is an undercover alliance fed on board. In the second half of the original pilot, Simon struggles to save Kaylee, and in turn River and himself while Mal, Zoe, and Jayne attempt to unload the cargo from the salvage to a trigger-happy mayor of a border moon.
12Heart of Gold
The Serenity responds to a distress call from Nandi, an old friend of Inara's, who is running a brothel on the moon of Deadwood. The unsavory leader of the moon's only town where the brothel is located has gotten Petaline, one the girls, pregnant and is demanding that he be given the baby. Nandi enlists the help of the crew of Serenity to defend the brothel and keep the baby with it's mother.
When Mal bumps in to his ex-wife, Saffron, he has to make a difficult decision whether or not to trust her as she offers the crew the chance to make a handsome profit from a mission that will take them to the planet Balerephon, where they'll have to steal a heavily guarded, priceless Earth antique. However, Inara does not trust Saffron from the last time (see 'Our Mrs. Reynolds') and plots with Mal to have an alternate plan. Meanwhile, Jayne is concerned that Simon and River will discover that he sold them out to the Alliance on Ariel.
A pleasant day out at a space station turns sour when Mal and Zoe receive the dead body of one of their old army buddy's in the post office. Their old friend is named Tracey who fought with them during the Battle of Du-Khang during the Alliance-Independence Civil War six years earlier. Along with Tracey's body is an audio message, asking them to take him to his home planet to be buried by his parents. However, Mal begins to suspect something might be wrong when Alliance agents, led by the relentless Lt. Womack, start chasing Serenity, demanding return of their property: the body. It soon turns out that Tracey is actually alive and reveals the real reason why he faked his death, and why he's going to die soon.