Logan and Martha put their clothes back on after having sex.
Jack takes a chopper pilot uniform from a locker in the outbuilding. Chloe lets Jack know that she and Novick found a way to pull the co-pilot from the flight.
A Secret Service agent removes the real co-pilot from the helicopter because there is something wrong with his paperwork.
Novick prepares Jack's Marine One identification papers. Martha lets him know that she has stalled Logan as much as possible. Novick calls Pierce and warns him that the reassignment documentation is being faxed to the outbuilding.
The co-pilot enters the building to find out about his paperwork. Jack knocks him out.
Wearing the uniform and the pilot helmet, Jack walks out and shows his paperwork to the agent on duty. He boards the chopper.
The Presidential limo pulls up to the outbuilding. Novick has Martha find an excuse not to be on board. She tells her husband that she thinks he should step out of the helicopter alone because it will make for a better press image. Logan agrees, and gets on the chopper. It takes off.
Once the helicopter is in the air, Jack warns the pilot that he will kill him if he doesn't keep flying. Jack orders him to dismantle the flight communication on his helmet.
Jack goes to the back of the chopper and stun guns the two Secret Service agents to make them pass out. He handcuffs Logan, who is shocked to see Jack.
Chloe radios to Jack a coordinate to land the helicopter at an empty warehouse. Logan asks Jack what he wants, but Jack remains silent. Logan goes on to try to explain his actions.
Chloe calls Morris, who is heading towards where the chopper will land. She instructs him to handoff something when he arrives.
The pilot lands next to a warehouse and shuts down the chopper. Jack stun guns the pilot, who passes out.
Jack forces Logan into the empty warehouse. Logan tries to bribe him. Jack removes all the objects from Logan's pockets and cuffs him to a pole.
The confused Morris pulls up to the chopper and goes inside the building. He carries a briefcase.
Jack finds Morris and takes the briefcase and a piece of equipment from him. Morris sees President Logan and is stunned. Jack orders him to leave.
Jack calls Chloe and she tells him that he has less than ten minutes until the response team comes after the President.
Jack sets up a camera on top of the briefcase and tells Logan that he wants a confession. Logan insists that he will not do so. Chloe watches this over the video feed.
Jack starts to ask Logan questions about the Sentox gas being given to the Russian separatists. He wants to know the truth about the deaths of Palmer and others. Logan insists that everything he is saying is a lie. Jack lets him know that Cummings, Henderson and Nathanson all confirmed they were involved in a conspiracy before they were killed. Logan refuses to say anything, and accuses Jack of attempting to torture him. Jack tells him that he won't torture him but will kill him unless he confesses.
Jack recalls how, a year and a half ago, he was told his life was in danger and faked his own death to protect himself. Now he is sure that Logan was the source of this danger to his life. Palmer and the others who tried to help Jack are now dead. "I have absolutely nothing to lose," Jack says, assuring Logan that he has no problem shooting him. Jack is confident that Logan will face justice.
Jack raises his gun and starts to count to three. Logan is afraid, pleading that his death will only make him appear to be a martyr. Shaking, Jack gets to three but doesn't pull the trigger. Logan is relieved that Jack could not kill him.
Suddenly, a TAC team swarms the warehouse. Jack hears them and lowers his gun. He gets on the floor and puts his hands behind his head.
At CTU, Chloe types something and quickly shuts down her laptop.
The Secret Service captures Jack. Logan grabs all of the things removed from his pocket. He tells the agents that Jack is delusional and needs to be put in solitary confinement.
The naval chopper lands at the airfield where Novick and Martha are waiting. Novick tells her that Jack wasn't able to get the confession and is now in custody. Martha panics.
Palmer's casket is removed from a hearse with full pomp and circumstance. It is placed near a podium. Martha breaks down, accusing Logan of being a murderer. Logan has the Secret Service agents take her away into a hangar. "He's not fit to be President!" Martha cries out.
Logan goes to the hangar. He smacks Martha and checks to see if she's wearing a wire. Logan accuses Martha of delaying him with sex in order to get Jack on the chopper. He asks her why she did it. Martha explains that he had Palmer and others killed to hide his conspiracy. "I did it for the good of the country," Logan says repeatedly.
Logan threatens to fill Martha with drugs and send her off to an asylum if she tells anyone what she knows.
Logan and Martha emerge from the hangar and walk to the podium. He addresses the gathered military and press, boasting of his victories against the terrorists.
Buchanan and Karen are shocked when Chloe sets up a conference call with the Attorney General. She explains that Jack placed a listening device on the President. Chloe plays back the recording of Martha and Logan talking in the hangar. The President admits responsibility for the terrorist plot and for killing Palmer.
Logan eulogizes Palmer, calling him a "wonderful friend." A federal marshal guarding the ceremony gets a call from the Attorney General. The Marshal is confused by what is being said to him, but he agrees to obey the order.
As he speaks, Logan notices rumblings among the agents surrounding the gathering. The Marshal and the Secret Service descend upon the podium as Logan ends his speech. The Marshal whispers something in the President's ear and Logan's face goes white. The Marshal pulls out the fountain pen from Logan's pocket and shows him the microchip transmitter planted inside of it.
Logan turns to Martha and Novick, speechless. He is escorted from the podium amid the twenty-one gun salute to Palmer and is placed in a limo for arrest. The casket is loaded upon the plane.
At the warehouse, Jack sees Audrey emerge from a car. He rushes to her and kisses her. An agent interrupts Jack with a call from Kim. Audrey says she will wait for him outside.
Jack goes in the building and picks up the phone. There is no one there. Suddenly, a masked man comes up from behind and gags Jack's mouth. Jack tries to fight off the other masked men, but the chloroform in the gag makes him pass out. The men whisk him into a room and shut the door.
Karen tells Buchanan that she thinks Logan will resign and try to cut a deal for clemency. Since the Vice President will soon be sworn in as President, Buchanan thinks he will be fired. Karen says she will make sure that Buchanan is still running CTU. She apologizes for her behavior towards him earlier in the day. Buchanan invites her out for breakfast but Karen needs to go to Division for debriefing. She asks for a rain check.
Buchanan commends Chloe for her work and hands her something found in Edgar's possessions. It is a photo of her and Edgar. Chloe tears up. Morris comes up and kindly asks her if she wants to talk about it.
Audrey goes into the warehouse looking for Jack. She sees the phone off the hook and becomes worried. Audrey runs out and alerts the agents that Jack is missing.
A beaten and bloody Jack is dragged into a dark room. The men remove their masks and reveal that they are Chinese. Their leader is Cheng, the head of security from the Chinese Consulate who threatened the American government to turn over Jack for his raid on the consulate building eighteen months ago. "China has a long memory," Cheng says. "Did you really think that we would forget?" Jack can barely speak, but begs to make one phone call. Jack wants them to kill him, but Cheng says he is too valuable to kill.
Cheng has Jack kidnapped aboard a Chinese shipping boat. It is already sailing the ocean.