The episode opens with Serenity dead in space; her interiors in disarray and completely devoid of occupancy. The one exception is Captain Malcolm Reynolds, who falls to the floor of the cargo bay, bleeding from a stomach wound. The episode then launches into its varied flashbacks; though the events are presented in this synopsis in strict chronological order, (one era per paragraph), readers should be aware that the episode's narrative moves back and forth between all three eras.
The first era visited is the gradual assembly of the crew: Mal welcomes Zoe Alleyn aboard his new purchase, a Firefly-class transport, and quotes the words of the man who sold it to him: "You buy this ship, treat her proper, she'll be with you the rest of your life." "That's because it's a death trap," Zoe replies. Nonetheless, Mal declares his intention to renovate her, make her spaceworthy, and assemble a crew. The first two to join the team are Hoban Washburne, an accomplished pilot with an accomplished mustache which bothers Zoe, and a laid-back mechanic named Bester. On a layover for repairs, Bester brings a young woman to the engine room for some illicit coupling; this woman, Kaylee Frye, soon replaces him as engineer when she shows an instinctive rapport with the ship's engines, diagnosing during sex a technical problem Bester couldn't fix while paying attention. The next recruit is Inara Serra, who uses her status as a Companion (and the legitimacy it confers) to bargain for a 25% discount on the rent. She also insists that Mal never call her a "whore" again (an ironic reference to the fact that he calls her this at least once an episode). The final member is Jayne Cobb, a dumb but competent tracker and enforcer whose partners are cheating him out of his fair share; he defects with enthusiasm when Mal offers him a bigger cut of the payoff, and his own bunk.
The second timeline concerns events leading up to Mal's predicament. The crew has assembled in Serenity's mess hall for dinner, including a birthday cake for Simon. Sudden alarms precede a wash of fire blasting down the corridor from the engine room; Zoe makes a diving leap to save Kaylee from flames, while Mal hurries to the bridge, seals off the ship's upper levels, and vents the lower decks (and the fire) out the hangar bay. Zoe has been gravely injured by her daring rescue and must be revived with a shot of adrenaline to the heart; Wash is shaken by his wife's condition, but Mal exerts his authority to keep him focused. Kaylee, meanwhile, discovers that the engines, as well as both primary and secondary life support, are offline; the problem is the "port compression coil," a part she mentioned as being in poor condition as far back as the pilot episode and which has since given out. At Mal's insistence, she attempts to fit it back onto the engine, but even he can see the part is damaged beyond repair. This leaves Serenity with only a few hours of oxygen left (though, as River helpfully reminds Shepherd Book, "We'll freeze to death first"). Thus, Mal makes the decision to abandon ship. The other eight crew members are to take the ship's shuttles and fly in opposite directions, hoping to flag some help, while he stays put in case somebody answers their distress call more directly. Wash rigs a big red button on Serenity's helm, which Mal can push to call everyone home again.
Mal settles in, eventually being woken by an answer to the distress call. He and the captain of the other ship bargain for a new compression coil, but when the captain sees that Mal is telling the truth, he shoots Mal and decides to commandeer Serenity for himself. Mal turns the tables by grabbing a nearby gun when their backs are turned, leaving him in the condition seen in the episode's opening: on the floor of the cargo bay, bleeding from a stomach wound.
Mal goes to the infirmary, where he fortifies himself with a shot of adrenaline straight to the heart. He then proceeds to the engine room, where he manages to get the port compression coil installed correctly, thanks to Kaylee's earlier demonstrations. Finally he staggers up to the bridge, but is unable to press the big red button before blood loss takes him. As Mal hears the voices from the various flashbacks, he gradually comes to in the infirmary, where the crew is bustling about. A supine but conscious Zoe welcomes him back to awareness. She takes responsibility for ignoring his orders and returning to Serenity, and promises not to do it again. As Mal drifts off again, he asks if "you all gonna be here when I wake up?", and Book assures him that they will.
The episode closes with, chronologically, the most remote flashback, in which Mal is still contemplating which ship to buy. The used-vehicle salesman is in mid-pitch: "You buy this ship, treat her proper, she'll be with you the rest of your life... Son. Hey, son, you hear a word I been saying?" Mal has not; he has turned his back on the salesman and the flashy yellow rocket-like vehicle he is trying to sell, and is staring, instead, at the final and most important member of his crew: a broken-down Firefly-class transport, abandoned at the edge of the lot...