George returns to CTU where he orders the medics to revive a badly injured Paula, who has vital information.

Palmer comes down hard on Eric for his deception.

Kim takes Megan to the hospital, but the staff accuses her of abuse.

Jack locates the leader of the American terrorist cell. He learns that the woman who gave them inside information on CTU is an old enemy.

The team arrive on a new planet and find diamonds. The team soon starts arguing over the diamonds themselves – a concept which Draga has trouble understanding. While Gus explains the concept of «  »money’ at great length, a team of bounty hunters closes in on the SG crew. Gus and Draga get captured but Gus turns the mercenaries against each other by playing on their greed. The team manages to overcome their greed and get it together to help out Gus and Draga but have to give up the diamonds to the mercenaries to buy their friends’ freedom.

The crew visit the planet Ariel because Inara needs to receive an annual Companion physical. The crew is offered a surprising job by Simon: in return for stolen medicine he wants them to get him into a hospital to use a high-end scanner to diagnose River. Simon devises a plan – Kaylee and Wash browse through the local dump and find parts to make an imitation emergency vehicle so the crew can get into the hospital posing as EMTs. Simon and River pose as corpses with the aid of a drug Simon has. While Mal and Zoe round up some medicine, Jayne stays with River and Simon, who are unaware he has ratted them out to the Alliance in return for money.
Jayne rushes Simon through the examination and on the way out Jayne, Simon, and River are caught by the Alliance. Jayne is betrayed by the Alliance and becomes a prisoner himself. They manage to escape as the Men With Blue Hands arrive and ruthlessly execute anyone who had contact with the Tams. Mal and Zoe end up saving their friends and Simon ma

Jack warns Lynne about the impending bombing of CTU, but her efforts to alert Palmer are sabotaged by Eric, who has his own agenda.

George locates the warehouse where the nuclear bomb was built, but his discovery results in an unexpected tragedy.

Kim takes Megan to CTU, believing that it is the safest place for both of them.

Right after arriving on a new world Draga gets a sense that something is watching them. Harrison finds a Mayan temple and returns to report he found the T’ak’khan and a captive human prisoner. However, Seattle and Stacey become suspicious when Harrison acts differently. Gus decides to launch a solo rescue and finds the prisoner is Captain Arnold Grimes – then he gets captured and is thrown in the cell with the real Harrison – they discover a race of shapeshifters who are reluctantly helping the Tlak’khan. Gus puts the pieces together and realizes how he was framed, then engineer an escape while the shapeshifters/Gus & Harrison lead the others into a trap. They escape and go rescue the team from a battle with the shapeshifters, seeing through the fakes. They are about to leave with Grimes when Draga says that she still senses a presence. Gus told everyone to whisper their suspicions in his ear so that he could find out who it was. The only person who accused someone else was Grimes – f

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.