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On a planet, Simon is kidnapped by locals who need a doctor, while River is threatened with burning as a witch.

Jack works to establish his cover with a small group of domestic terrorists. He learns that their target hits very close to home.

Kim takes Megan and runs from the house, but Gary pursues them.

Palmer and Eric disagree over how to deal with the media during the nuclear threat.

After avoiding a flash flood, Seattle finds a kitten-like creature that she names Flotsam. It gets into their food supplies and grows substantially…and grows some more. All efforts to train him seem in vain and it looks like the team will have to leave him behind. Da’kyll and his Tlak’kahn mercenaries show up and Flotsam gives warning by playing “”fetch”” with a grenade. A simlar flash flood wipes out the Tlak’kahn and Seattle agrees to leave Flotsam behind.

On the planet Persephone the crew contact their old “friend” Badger the ruthless crime lord to transport some goods on behalf of a local lord. While at a ball to arrange a transport job with the lord, Mal defends Inara’s honor when her current customer insults her. By local custom he unintentionally challenges her date, Atherton Wing, to a duel.

Over a year has passed since the events of Day One. President David Palmer is fishing with his son in Oregon when he learns of an emergency. He is taken to his underground bunker, where he learns that a Middle Eastern terrorist group known as Second Wave is planning to set off a nuclear bomb in Los Angeles
sometime that day.

At CTU, George Mason is ordered to contact Jack Bauer, who may be able to provide a lead to the terrorists.

Jack has been out of commission since the death of his wife. He is also estranged from his daughter Kim, who is now working as an au pair. He isn’t interested in returning to work, but changes his mind when Palmer personally requests his help.

Kim overhears her boss abusing his wife, so she locks herself and their little girl in the bedroom. Gary forces his way in and attacks Megan.

A young girl named Marie is marrying a man who may have connections to the leader of the terrorist group.

At CTU, Jack learns that the key to finding the bomb rests with a group of American terrorists whom he infiltrated once before.

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.