Serenity, Part I
Mal Reynolds, a veteran of the War of Independence, is captaining a Firefly-class boat, the Serenity. He and his crew Zo, one of his fellow "browncoats"; Jayne, a mercenary; Wash, an ace pilot and Zo's husband; and Kaylee, a crack mechanic are salvaging a dead ship when an Alliance vessel detects them. They get away, but the Alliance bulletin about their doings means their cargo is now too hot to sell. They take on passengers on the planet Persephone, including a doctor named Simon Tam, who is carrying a large piece of cargo; a shepherd who calls himself Book; and a man named Dobson. En route to find another buyer for their loot, Dobson reveals himself to be an Alliance agent. He's not after Mal and his crew, but Dr. Tam and his cargo. Dobson shoots Kaylee, then Dobson is captured, with surprising help from Book. Simon agrees to operate on Kaylee only if Mal helps him flee the Alliance. Mal opens Simon's cargo which turns out to be a naked woman.

Serenity, Part 2
The naked woman is Simon's sister, River, frozen cryogenically. Simon reveals that River was attending what was supposed to be an Alliance academy, but while she was there they experimented on her brain. Simon spent his fortune breaking her out of Alliance custody and is on the run. Mal brings the Serenity to the planet Whitefall to try to sell the cargo they stole from a derelict ship. Their buyer double-crosses them, but Mal's prepared, and they get their payment, pausing to shoot Dobson and leave him for dead on the way. They also encounter Reavers (a savage and dangerous race of cannibalistic humans that travels the edge of colonized space and beyond), and have to escape them with some fancy flying by Wash. Mal invites Simon to stay on board as the ship's medic.

The Train Job
The crew of the Serenity, in economic distress, takes a job from a cruel gent named Adlai Niska to rob a train. Mal doesn't ask the particulars, which Niska appreciates. However, when Mal and Zo board the train posing as regular passengers, they discover their first wrinkle: Alliance guards. Mal is thrilled at the notion of stealing something from under the Alliance's nose; Zo's a bit more worried. Regardless, they successfully pull off the heist. Before they leave the planet, however, they learn that what they stole are medical supplies that are desperately needed by struggling colonists on this world. After Inara helps liberate Mal and Zo from custody all the robbed train's passengers are being held Mal decides (over Jayne's objections) to give back the supplies to those who need them. The good deed done, Mal sends Niska's thugs back to him empty-handed.

A friendly basketball game aboard Serenity is interrupted by an encounter with a colony ship that appears abandoned. When the crew investigates, they find plenty of supplies, meals left half-eaten, the lifeboats all gone and then, eventually, mutilated bodies, and one half-crazed survivor. Mal's theory is that Reavers attacked, which doesn't sit well with the crew. Simon and Book give the colonists a proper burial, Jayne loots the ship, and Kaylee removes a Reaver booby-trap. Meanwhile, the survivor lays in the infirmary. All's well until the Serenity encounters an Alliance ship. While Simon and River hide outside Serenity in EVA suits, the crew is questioned, Serenity is searched, and the survivor is taken aboard the Alliance ship. Things look grim for the crew, right up until the survivor who has seen such horrors that he transforms himself into a Reaver in order to cope with the trauma escapes back to Serenity, leaving a swath of bodies. Mal convinces the Alliance commander to let him join the search team, and Mal saves the commander's life by killing the crazed survivor. In return, the commander lets the Serenity and its crew go...but he impounds all their cargo.

Serenity returns to Persephone for a dual purpose: Inara has a client and the crew has a job. Badger, who had previously refused to fence the Serenity crew's goods, now comes to Mal hoping he will broker a deal to move some cattle offworld to Jiangyin. Sir Warwick Harrow refuses to deal with so low-born a gent, but Badger thinks that Mal is respectable enough for Sir Warwick to speak to. Badger gets Mal an invite to a party, which he attends, with a lushly dressed Kaylee as his date. Inara is also present with her client, Atherton Wing, who tries to convince her to be exclusive to him. While Kaylee is shunned by the women at the ball but bonds with the men-folk over engineering minutiae Mal objects to the attention that Wing lavishes on Inara, which leads to violence. Violence leads to a duel with swords, an instrument Mal is ill-equipped to handle. While Badger holds Serenity's crew hostage to prevent a rescue, Inara tries to give Mal a crash course in swordfighting, which almost works. Somehow, Mal manages to win the duel, Inara blacklists Wing with the Companion Guild, and Sir Warwick agrees to hire Mal and his crew for the job.

In the past: When Simon and River were children, the Tam family was happy. River, a genius, got along famously with her older brother, and they didn't want for anything. But when River went to the academy, things went sour something only Simon could see, because their parents refused to believe that anything was wrong, even though River's letters were begging for Simon's help via an esoteric code known only to the two of them. In the present: On the Serenity, River's outbursts are growing worse and disturbing the many cattle in the hold. The cattle are offloaded safely on Jiangyin, and Simon and River go into town. However, Mal and the crew run into trouble with the locals; Book is shot, and Simon and River go missing. The doctor and his sister have been kidnapped by hill folk, who want Simon to treat them. With no choice, he does as they ask. Meanwhile, Serenity makes a hasty takeoff to find a medical facility to treat Book. To everyone's surprise, Book's ID gets him VIP treatment at an Alliance facility, no questions asked. To Simon's surprise, River shows enough evidence of psychic powers that the God-fearing people of Jiangyin decide to burn her as a witch. Only the timely return of the Serenity spares the Tams from a fiery death and convinces Simon that, for better or worse, he really is part of Serenity's crew.

Our Mrs. Reynolds
Mal, Jayne, and Zo drive away some bandits from a settlement on Triumph, leading to a raucous celebration. The next morning, the Serenity crew takes off, only to find themselves with an additional passenger: Saffron, who claims she is Mal Reynolds' wife part of Triumph's payment for services rendered, apparently. Book verifies that a portion of their drunken revelry was a marriage ceremony. Mal finds himself in a quandary: He is saddled with a wife he doesn't remember marrying and who is devastated by his rejection, and a crew that is alternately teasing and excoriating him. He tries to free her, but her insistence on being a proper wife wears Mal down to the point where he kisses her. That's when things get really bad: Mal falls unconscious after their kiss. Saffron is a con artist who wants to sell the Serenity for scrap, and she comes dangerously close to doing so.

A job on Canton, where the local mud is harvested as construction material, has Jayne rather nervous, because on his last trip to this moon he stole the magistrate's money, only to be forced to dump the cargo in order to break free of the atmosphere. However, to everyone's surprise, and everyone save Jayne's amusement, there's a statue of Jayne in the town square. Later, the crew is regaled with an immensely popular local song, "The Ballad of Jayne," which praises him as the hero of Canton. His loot was dropped right on the "mudders" the common folk of Canton who assume Jayne did it on purpose, Robin Hood-like. Mal uses Jayne's newfound status as a distraction to allow them to complete the new job. Unfortunately, the magistrate that Jayne robbed is less amused, and he frees Jayne's partner from captivity in order to get revenge, leading to a brutal and tragic confrontation in the town square.

Out of Gas
A bleeding, dying Mal Reynolds tries desperately to get to Serenity's engine to install a part. As he struggles, alone, through the abandoned ship, he alternately recalls how he got here, and how his crew was assembled. Serenity isn't flight-worthy when Mal buys her, a fact that Zo is quick to point out. Things don't go much more smoothly from there, as Zo doesn't like the mustachioed pilot named Wash, though Mal raves about him, and their "genius" of a mechanic Bester can't seem to fix what ails Serenity. Things soon start looking up: Bester brings aboard Kaylee, who promptly diagnoses what ails the boat, prompting Mal to give her Bester's job while Zo gives Bester the boot; Wash, currying favor with Zo, shaves his mustache. Later, the crew recruits a mercenary named Jayne, who gets the drop on Serenity while he is in the employ of a gent named Marco. Mal and Zo convince him to switch sides by offering him better pay and accommodations. A fire aboard Serenity cripples her engine, injures Zo, and uses up a sizable chunk of the remaining air. Kaylee needs a part she doesn't have. Everyone save Mal abandons ship in the two shuttles, while Mal hopes for a rescue which, surprisingly, comes and, unsurprisingly, becomes a double-cross that Mal escapes only after being shot in the gut.

The Serenity's latest job comes from an unlikely source: Dr. Simon Tam. He needs to break into a hospital on Ariel so he can scan the ever-deteriorating brain of his sister, River, and try to figure out what the Alliance did to her. For Mal and his crew, the rewards will be a stash of incredibly valuable, central-planet medical supplies that are hard to acquire on the rim, and which can be resold for a hefty profit. However, Jayne has his eye on an even greater reward: A bounty from the Alliance, which still wants River back. Jayne turns over River and Simon only to find himself a prisoner, as well, with no hope of collecting his reward and every expectation of a very long and miserable incarceration. Jayne contrives a narrow escape for himself and the Tam siblings, and the crew is reunited on Serenity. Mal, however, has figured out why the job went bad, and he makes clear to Jayne what happens to those who betray him or his crew.

War Stories
Wash grows increasingly frustrated with hearing stories of the "good old days" when Mal and Zo served together, and generally with the fact that his wife seems to have a stronger bond with her captain than with him. Wash forces himself to accompany Mal in Zo's stead on a job which then goes sour, when Mal and Wash are captured by Niska, who still holds a grudge over Mal not delivering on the train job. Niska tortures Mal and Wash. Zo arrives to negotiate for their release, the crew having pooled their earnings from the job on Ariel to ransom their shipmates. Niska, however, feels the sum offered is enough for only one of them, and she must choose who to save. Without hesitating, Zo chooses Wash. Niska reconsiders and says it's enough for part of one other so he also gives her Mal's freshly cut-off ear. The financial option having crapped out, the crew mounts a rescue, including the surprise participation of Book and later, the deadly participation of River, who saves Kaylee's life by shooting three snipers with her eyes closed. Meanwhile, though Niska gets away, Mal is saved, and Simon is able to reattach the captain's ear.

While exchanging contraband with fellow rogue Monty another former "browncoat" Mal meets Monty's new wife. To Mal's shock, it's Saffron, now calling herself Bridgit. Monty is not thrilled to find out that his wife also married Mal once, so he leaves her behind on the moon with Mal while the latter waits for the Serenity to return. Frustrated with Inara's complaints about Mal not flying to worlds where she can entertain clients, Mal brings Saffron aboard with a job she insists will provide them all with tremendous wealth: stealing a "Lassiter", a rare old laser weapon, from a collector on Bellerophon. Kaylee comes up with a method of getting the Lassiter out of the estate without the sensors detecting its departure: by throwing it out with the garbage, then having Serenity intercept the trash carrier. Mal and Saffron infiltrate the estate and start to make the theft, when Durran, the owner, walks in and recognizes Saffron as his wife, Yolanda. Mal, not entirely surprised to meet yet another husband of Saffron's, quickly pretends to have "rescued" Yolanda, who went "missing" some years before. The tables are soon turned, and Mal and "Yo-Saff-Bridg" depart with the Lassiter, tossing it in the disposal. Saffron then double-crosses Mal, taking his sidearm and leaving him naked in the desert. When Saffron arrives at the trash can, though, she finds nothing, even after digging through all the filth. Then Inara arrives with the Lassiter, which she claimed before Saffron arrived, as Mal planned from the start the Serenity crew has conned the con artist.

The Message
At a space station, the crew shops, pokes around, and picks up mail. Jayne gets a letter and a knit cap from his mother, and Mal and Zo get a corpse. The corpse's name is Tracey, and Mal and Zo served with him during the war. He had left a recording, requesting that his remains be brought home to St. Albans. However, a Fed named Lt. Womack also wants Tracey's corpse, and he's willing to shoot down the Serenity to get it. Reluctantly, Mal orders an autopsy while Wash evades Womack. The most shocking discovery of the autopsy is that Tracey's alive. He was in a suspended state that simulated death and now he says he wants to get home, but he's carrying transplantable organs that need to incubate in a person. He decided to take a better offer on the black market, but the new buyer was caught, so Tracey "killed" himself and had himself shipped to Mal and Zo. Womack, having grown tired of Mal's stalling, resumes shooting at Serenity. Eventually, the crew realizes that Womack won't stop until they're dead but Book also notices that Womack hasn't checked in with the local Fed base. Tracey doesn't like the crew's plan, and shoots Wash to keep him from contacting Womack, which results in Zo shooting Tracey. Wounded, Tracey runs and takes Kaylee hostage, but Mal is able to gun him down, leaving Womack empty-handed and a threat from Book to alert the Fed base to Womack's extracurricular activities leads the Fed to depart Serenity in peace. The crew returns Tracey's body to St. Albans for proper burial.

Heart of Gold - SCRIPT
Inara gets a call from an old friend Nandi, who has left the Companion Guild and opened a whorehouse. Nandi's place is being threatened by Ranse Burgess, who impregnated Petaline, one of Nandi's whores, and is claiming the child. Nandi offers to pay the Serenity crew to help protect them. Mal's instinct, after meeting Burgess, is to skip out and avoid this mess, but Nandi refuses to give in. So the Serenity crew helps fortify the whorehouse save for Simon, who is busy delivering Petaline's baby. Nandi and Mal share a night together; in the morning Burgess attacks. Nandi is killed in the melee, but the Serenity crew and the whores emerge victorious. Petaline kills Burgess herself, right in front of his newborn child.

Objects in Space
River wanders the corridors of Serenity. She observes the members of the crew and in some cases eavesdrops on their thoughts or, in the case of Wash and Zo, their passions. She then, somehow, gets her hands on one of Jayne's guns. Mal disarms her, but this display leads Kaylee to tell everyone what River did during their rescue of Mal from Niska. Mal is convinced River's telepathic, and, despite their skepticism, the others tend to agree. Everyone goes to bed while Mal thinks on the matter. His mental perambulations are interrupted by a bounty hunter named Jubal Early, who boards the ship. He takes down Mal, and locks him in his quarters, and also locks Jayne, Wash and Zo in theirs. Kaylee is in the engine room, and Early terrorizes her and ties her up, then neutralizes Book. Finally he escorts Simon at gunpoint around Serenity to find River, who isn't in her bunk. She isn't in Inara's shuttle, but Early confines Inara, as well. Finally, River "shows" herself, as a disembodied voice, telling Early that she has blended her consciousness with the ship. She has become Serenity. It's a bluff, however she's on Early's ship, stalling him while she wakes up the crew and gets them to take care of the bounty hunter. Eventually, Early is left tumbling through space, while River is welcomed back by the crew.