After a flashback to Zoe’s and Mal’s days in the wars six years previous, we cut to the modern day where the Serenity crew is running a salvage operation on a deserted ship and are forced to flee with the cargo when the Alliance show up. Their buddy Badger refuses to buy the cargo so they head off to the rim worlds after picking up three passengers: Book, Simon, and Dobson. En route someone sends a signal to the Alliance and it turns out to be Dobson, an undercover Federal agent, who arrests Simon but is glad to take the whole crew in. He shoots Kaylee before being captured, and Simon forces Mal to flee in return for his doctoring services. When Mal investigates Simon’s cargo he finds a naked woman…

Kim and Miguel are arrested and the police plan to take them back to LA.

Tony questions Bob Warner at CTU and learns more about his government connections.

Palmer discovers a traitor in his ranks when the journalist whom he was holding is set free.

Nina pulls a deadly countermove, setting herself up as the main player in the search to locate the bomb.

A bounty hunter boards the Serenity to capture River for the Alliance.

Jack forces Nina to help with a sting operation against her contact in the hopes that he can lead them to the bomb.

Palmer and Mike try to gage Stanton’s loyalty when they investigate the chopper crash.

George has a final conversation with his son.

Major Bonner’s team arrives at a world destroyed by its inhabitants. Kreeda, the inventor, attempts to save what’s left of her civilisation—even if it means stealing and lying. Ec’co acquires a sympathy for her, but the next day the team finds their power sources stolen. Kreeda is the obvious suspect. She wishes to make up for her previous actions and warns the team about Tlak’kahn warriors nearby—but will they listen?

Jealous of Zoe’s relationship with Mal, Wash insists (thanks to a bit of scheming) that he go with Mal to try to sell some of the medical supplies the crew stole from the Alliance. In the middle of the deal Mal and Wash are kidnapped by men working for Niska the crime lord, who wants revenge against Mal for the botched train heist. He tortures Mal and Wash until Zoe shows up offering money in exchange for the prisoners. Niska says that the money is only enough for one person and Zoe chooses Wash. Wash realizes that Mal’s antagonizing him while they were being tortured was to help keep him alive and kicking. This inspires him to do everything he can to help Zoe rescue Mal from Niska. The rest of the crew jump on board to save the Captain.
Meanwhile Inara extends her services to a council member. To the crew of Serenity’s surprise, it’s a woman. And Simon continues to treat River with some of the medicine he stole but she suffers the occasional relapse as well as displays a penchan

Jack begins his interrogation of Nina and pushes all boundaries in order to force her to divulge the name of her contact.

Palmer is surprised and suspicious when his ex wife Sherry returns and claims to have information about a conspiracy against him from within his own administration.

Kim and Miguel plan to kidnap Megan from the hospital in order to take her out of LA and away from the nuclear threat.

Gus brings the gang to Brianna for some rest and relaxation and they’re caught in an earthquake. Harrison, separated from his jet pack, is rescued by Havave and helps him on his Kamuna initiation ceremony, while Ec’co discovers the volcano they are near will explode and destroy the local island. Harrison tries to convince Havave not to give in to peer pressure while helping him deliver an egg to a local creature as part of the rite, but they fail. He and Havene meet up with the others and the Akua, Havane’s people. The Akua initially refuse to leave but Havane’s actions convince them and they accept him despite his failure. The team manage to get to the Gate just in time as the island is destroyed.

George refuses to allow Jack to assist in Nina’s interrogation. Jack resorts to blackmail to change George’s mind.

Palmer and Stanton meet with a Middle Eastern ambassador who may be in league with Second Wave.

Tony visits the Warner home and questions Reza about his possible connection with Syed Ali.

Arriving on a new planet, the team meets with the Alteri, a martial society that practices ritual combat. After getting defeated several times, Stacey learns their ways and that wearing the «  »Mandro stones » » enhances the wearer. As she dons them she begins to suffer strange side effects – paranoia, anger, addictive qualities, and physical transformation. Stacey goes berserk and escapes for the Stargate. The team manages to slow her down enough so Gus can talk her down and Draga can transform her back to normal. Meanwhile, Draga has a vision of a star system after touching the stones which they believe may be the home of the Ancients.