Arriving on a new planet, Stacey runs into a web and reveals she has a problem with her fear of spiders. Naturally, the local civilization are spiders and Stacey apparently overreacts, injuring one of them and endangering relationships between the two groups. Stacey insists she acted in self-defense but is placed on trial for her actions. Meanwhile, the Tlak’kahn warriors show up and attack. Stacey comes to terms with the spider she harmed, allowing it to heal. She and it team up to help the team bring down the Tlak’kahn and the team departs.

In a delirious state after Serenity’s engine explodes, draining the ship of its oxygen supply, Mal has a series of flashbacks about how he came to own Serenity and form his crew.

Arriving on a waterworld, the team makes for a nearby island after losing one of their vehicles while Da’kyll reports to Hah’lak that he knows where Draga is. The councilman sends a pair of bounty hunters after them behind Da’kyll’s back. Ec’co, Draga, and Seattle get captured by the local amphibious natives and take the rest of the team to meet them. The locals, the Su’ri, welcome them once they are sure of the «  »landers » »‘ motives. The bounty hunters negotiate with Sargall, one of the younger members, to have him turn over the team in return for medicine. Driven by jealousy toward Harrison, Sargall helps the mercenaries by helping them capture Seattle to lure in Draga and then challenges Harrison to a dangerous race. While Gus tries to rescue R.J., Draga gets captured and Ec’co and Stacey give pursuit. Harrison rescues Sargall from a monster and then Gus leads the monster to the escaping mercenaries as they enter the Stargate without their captives and it ends up attacking a waiting Ha

Serenity sets down at the mudder colony of Canton where it turns out Jayne is a hero for having dropped a bunch of money there years ago that he and his partner Stitch stole from the local magistrate. The drop was unintentional but Jayne doesn’t turn down the attentions. Meanwhile, Kaylee and Simon dance, River rewrites Book’s bible, and Inara beds the magistrate’s son, a virgin.

The team intervenes on a planet when one group of the locals, the Mystari, use high-tech weapons to attack another faction – they meet up with Shepherd, a former Stargate team member who trained Gus. Shepherd claims the faction his men attacked are bandits but his followers worship him. Gus overlooks his apparent abuse until Stacey brings him around. Knowing Gus will act against him, Shepherd summons the Tlak’khan but when he finds out they plan to kill the team he and the locals side with Gus. Shepherd tells the Mystari to find their own way and then takes off on his own.

When the younger team members reminesce about birthday’s, Ec’co thinks back to his own torn life. The team convinces Gus to take Ec’co to his homeworld. An electrical storm shorts out their Stargate while Gus and Ec’co get taken into custody by the hostile Hrathi, who know of Gus’ alleged betrayal. The rest of the team rig a way to recharge the Stargate using lightning while the Tlak’khan launch an attack on the Hrathi. Gus helps to drive them off and then are taken to a cache of data crystals. It turns out the crystals are a fake, but one of the Hrathi reveals he is a shapeshifter. Gus and Ec’co pass the test and receive the real Tlak’khan data crystal they need.

While completing a job on a backwater world, Mal is married to a village girl without his knowledge. The girl, Saffron, gets onboard and the crew does not find her until they’re already in the air. Mal is not sure what to do with her, but let her come along.

The team arrives with a planet with a mysterious «  »Guide » » stone which is immediately endangered by an earthquake. The team helps the natives, the Mou’a’dash, to recover it. While Harrison deals with being «  »owned » » by a local native that rescued him, the Tlak’khan launch an attack. Gus, Draaga, and Seattle get captured and taken through the Stargate along with the Guide, which they use to travel to the Ancients’ home planet. They end up in a hellworld trap set by the Ancients, where the Stargate has no controls and they are stuck. Draga manages to use her powers to open the Stargate, leaving the Tlak’khan stranded. Gus realizes the Tlak’khan must have access to his travel record through the traitor and heads off to a planet he hasn’t been on before.

On a salvage mission aboard a drifting colony ship, the Serenity crew find signs that the crew were killed by the cannibalistic Reavers. They find one survivor, but things take a turn for the worse when an Alliance ship looking for an unspecified Firefly-class ship with brother-and-sister stowaways shows up and takes them in.

The team stay on a jungle planet, cut off by Nephestis who has framed Gus as a traitor. The local Thorn aliens are dying of a disease which Gus believes he left there on a previous expedition. The others choose to head out with the Ancient chrysalis but are ambushed by the Tlak’khan but escape…as the chrysalis hatches and the winged Ancient escapes. The Tlak’khan leader De’kyll takes the Thorn village hostage and Bonner surrenders but the Ancient intervenes and the cadets take them prisoner (except De’kyll escapes). The Ancient learns English through Seattle and asks the team for help, and after being named Draga. Draga heals the ailing Thorn but knows nothing about the Stargates and remains with the team.