President Logan reinstates Jack to CTU when he learns that the US(not Russia) is in danger. Jack captures and must negotiate with a scientist who helped Bierko open the nerve gas canisters. President Logan must decide how to handle revealing Walt's complicity to the public.
Bierko contacts President Logan and demands information about the route of President Suvarov's motorcade. Jack races to protect a witness who helped supply Bierko the nerve gas cannisters before Bierko has him killed.
Homeland Security takes control of CTU. President Logan orders martial law. Wayne Palmer goes to meet with Aaron Pierce. Jack interferes with a German spy's undercover operation while searching for Bierko.
CTU makes Christopher Henderson their priority while dealing with the restructuring into Homeland Security. Jack and Wayne must save Evelyn Martin's daughter in order to get crucial information about the conspiracy.
Jack and Wayne must retrieve a digital recording from a safe deposit box before Henderson's men get to it. President Logan starts to cover his tracks when he orders Homeland Security to issue an arrest warrant for Jack.
Jack and Audrey show Secretary Heller the recording but are shocked by the actions he decides to take in handling it. Karen Hayes works to cut off Jack's support inside CTU. Mike Novick begins to become suspicious of President Logan's actions.
Jack and Buchanan work outside the chain of command by recruiting Curtis for help. Homeland Director, Karen Hayes, begins to see discrepancies in the President's actions and begins to suspect his motives.
When President Logan realizes that he's been backed into a corner, he resorts to a drastic solution. While Karen becomes an ally in Jack's quest to expose Logan, Miles changes allegiances, and a villain from the past returns.
Vladimir Bierko manages to escape custody and take control of a submarine, the Natalia, bent on getting his revenge against the US. Jack reluctantly teams up with Henderson in hopes of getting a lead on Bierko, while Martha helps Aaron.