A man and a woman enter a hotel room making out. Everything is passionate until the woman breaks the man's neck. She then takes out all kinds of technical equipment and takes a scan of the man’s hand. The man's ID-card on the floor reveals his identity as Donald Frick of the Department of Defense.
A few hours later, James Sutton, the head of CTU Washington, notifies agent Martin Kail of this development. He does a double take when he sees surveillance footage of the woman.
The suspect appears to be Susan Walker, Martin’s CTU partner and former lover. Martin refuses to be put on the case, but because of a possible link with the kidnapping of James Heller (see Season 4), Sutton wants his best agent. Unexpectedly, Susan calls their office.
Susan warns Sutton and Martin not to come after her. CTU analyst Kelly traces the call and determines the location.
Martin goes to the location Kelly gave him. There, he finds a man whom he subdues. He also finds a router and realizes Susan was never there, but was just routing her calls through the place.
Martin questions the suspect, Christopher Gerber, with force. He refuses to talk, fearing what his employers would do to him. Gerber manages to untie himself, gets his fingers around Martin’s trigger and commits suicide.
Martin calls Kelly and has her do a background check on Gerber. A name and address of an accomplice pops up, arms dealer Oliver Krakowski.
Martin arrives at the Krakowski's address, who is just returning home with groceries. When he stumbles upon Martin, he makes a run for it. Martin chases him and is able to corner him. However, Krakowski is shot. When Martin turns around, he sees Susan, who knocks him unconscious.
Martin awakes in a cell handcuffed to a hand rail. He hears Susan talking in the next room about receiving payment from a man called Navi Araz. Martin manages to get his handcuff off of the rail, but not without alerting Susan.
Susan enters the cell because Martin is nowhere to be seen. When she checks under the bed, Martin shows up behind her. A fight ensues and Martin manages to get the upper hand.
As Martin questions Susan, she explains that there's a conspiracy involving the Department of Defense and another government agency and that Sutton is involved in it. When he refuses to believe it, she tells him that Sutton has been receiving payments from Navi Araz. He then tells him to check Sutton's transactions with Bolivian International Finance.
Martin has Kelly investigate Sutton's transactions, but she is unable to hack the banking agency. When he asks her to see if Sutton has tried to access his account from his computer, she finds a series of transactions from a N. Araz. She also finds a secured file called "Blind Justice" that can only be accessed from Sutton’s computer. Martin decides to return to CTU.
Martin lures Sutton out of his office and breaks in. He accesses the file for the program, an operation known as "Blind Justice", and finds the names of other DoD agents: Chris Jarvis, Kenneth Proctor, and Steven Kinsey.
Martin bumps in to Sutton who tells him about two other dead DoD agents, Proctor and Kinsey, which might be involved to the attempt on James Heller. Martin recognizes Susan has been telling the truth, but tells Sutton he'll let him know as soon as he finds Susan.
Martin returns with Susan and tells her about the other DoD agents. She then explains him that the agents are part of a team that can complete a numeric sequence to launch a series of nuclear missiles. To do this, they need the agents' palm prints. She explains that Frick was planning to sell his print, making his murder necessary. Susan tells him they must find the remaining DoD agent before it is too late.
When they arrive at the house of the final agent, Chris Jarvis, the front door is open. Inside, they find Jarvis dead with his hand cut off. Next to him is a broken palm-scanner. They figure it must have been broken in the struggle, forcing the terrorists to take his hand.
Susan knows someone who can help them break into the DoD computers. This way they might be able to change the data so it is useless to the terrorists. While Martin drives, Susan calls the contact. He says he’ll be ready, and hangs up. He then hands his phone to a gunman who is holding him under duress.
Susan and Martin arrive at Susan’s contact only to find him dead. The blond-haired killer shows up and a gunfight breaks out. Martin manages to take the killer out, but the computer they need was shot in the fight.
Susan gets the computer to work. It will take about 20 minutes before the program will be able to make the changes. At CTU, Kelly is able to trace the computers signal at Sutton's command, and he demands her to dispatch a team to get them.
Just before the program is complete, Sutton enters with a TAC team and removes the key-card needed to erase everything. He proceeds to arrest Susan and Martin.
Back at CTU, Sutton questions Martin, who openly accuses him of the conspiracy. Sutton regards Martin's behavior as extremely inconsistent with his former excellent performance, which does not bode well for his future. He tells the guard to move Martin to holding.
In the holding room, Martin and Susan wonder why Sutton is still at CTU while he has everything he needs. They realize Sutton is not working with the terrorists, and everything is a setup. Only one other person has been involved with everything that has happened that day: Kelly. Meanwhile, Kelly finds Sutton, and shoots him dead with a sound-suppressed pistol.
In holding, Susan fakes a seizure while Martin calls for Matthews, the guard. He enters but Martin knocks him out and takes his sidearm.
Susan and Martin go to Sutton’s office because it is the only place where Kelly can send the info to the terrorists without anyone else noticing. They barge in and Kelly shoots Susan in her shoulder. Martin shoots Kelly dead and removes the key card before it is able to complete the transfer. However, Martin now realizes he is shot in the stomach and falls down. Susan catches him and yells for help while Martin lies in her arms.