Bierko's men flush out the Sentox gas aboard the sub Natalia. Bierko instructs them to begin the launch countdown. They are targeting high population areas to punish the Americans for allying with Moscow.
Audrey contacts Admiral Kirkland at the Point Mugu Command Center to alert him that terrorists have seized control of the Natalia submarine. All of the Navy crew onboard dead. She asks him to sink the Natalia with his F-18 fighter planes. Yet they won't be there in time before the missiles launch.
Jack, Henderson and the TAC team are at the dock of the Natalia. Since backup won't get there in time, Jack will have to stop Bierko himself. Henderson notices a signal tube launching off the side, which indicates someone on board is trying to send a distress signal.
Henderson tells Jack that he won't go on the sub unless he gets his own gun for protection. Distrusting Henderson, Jack is hesitant to give him a weapon.
Chloe scans the area around the sub for emergency frequencies and finds one coming from a survivor. She patches Jack to Rooney, a petty officer engineer aboard the sub. Rooney gives his location, and Jack has him go to an entry point where they can board. Rooney will have to kill the terrorist at that post to go unseen.
Henderson demands a gun, and Jack gives it to him. They head towards the sub.
Novick briefs Logan about Bierko raiding the submarine and taking over its missiles.
From outside the conference room, Martha watches Logan in the midst of the crisis. She calls Pierce and warns him not to remove the body from the retreat until she talks to Novick.
With less than ten minutes to missile launch, Jack asks Henderson how long it will take him to shut the system down.
Jack instructs Rooney on how to slit the throat of the terrorist guarding the door. Rooney clumsily attacks the man and kills him. He radios Jack that their entry is clear. Jack shoots the guard on the deck, and the TAC team runs to the top of the sub.
The missile doors open up on the top of the sub in preparation to launch.
Jack and Henderson board the sub and meet Rooney. He shows them where the control room is, and Jack has him access it from the other side to create a distraction.
Rooney knocks over a tool cart, causing a loud noise. Bierko leaves the control room to investigate. Jack and his team go in the control room and see one man left to arm the missiles. Jack stabs him in the throat.
Henderson gets to work on the controls, manually reversing the launch codes. Jack goes after Bierko.
Jack fires at one of Bierko's men. Chloe warns him that they have sixty seconds until launch. Henderson works as fast as he can.
The other terrorist knocks Jack's gun down. Jack grabs him and uses the man's arm to fire at Bierko. Jack shoots at a pipe that releases steam, and he presses the man's face to the burning pipe. Jack is set free from his grip. Bierko smacks Jack in the forehead with a metal tool. Jack leaps to a pipe above and uses his legs to snap Bierko's neck. Henderson is able to dismantle the missiles. Everyone at CTU sighs in relief, and Karen has Chloe call off the F-18 planes.
Jack returns to the control room, but Henderson is gone. He tells CTU to take him off of radio and he runs outside on the deck to look for Henderson. Henderson comes up behind Jack and makes him drop his weapon. "You weren't ever really gonna let me go, were you?" Henderson asks. He pulls the trigger and the gun clicks. Henderson realizes he's been had, and he removes the empty clip from his gun. Jack accuses him of killing his friends Palmer, Tony and Michelle. Then he shoots Henderson dead. Rooney comes out and is frightened when he sees what Jack has done.
Military transport vehicles arrive at the dock of the Natalia. Jack identifies himself and asks for a vehicle. He calls CTU, claiming to have killed Henderson in self-defense. Jack tells them he is coming back to CTU and asks Chloe to pick up.
Jack explains to Chloe that he is going after Logan himself and needs her help. Chloe agrees. Jack gets into the government car provided to him and drives off.
Logan is pleased when he finds out that Bierko and the missiles are no longer a threat. He wants to publicly address the crisis resolution before escorting Palmer's casket to Washington. Novick goes to prepare the statement.
Martha approaches Novick as he leaves the President's office. She asks whether he has been suspicious about Logan's actions. Martha begs him to come with her.
Logan is happy to report to Graham that Henderson was killed aboard the sub. "Mr. Bauer will be taken care of," Logan guarantees.
Martha brings Novick to the stables to see Pierce, whom Logan had ordered to be killed. Martha explains that Logan was involved with everything that has happened -- from Palmer's murder to supplying the terrorists with nerve gas to Cummings' fake suicide. Pierce says that Jack had a recording to implicate the President, which is why Logan wanted Jack dead. Novick begins to realize that all of this is true, and he wants to drive Pierce off the retreat. Pierce tells Martha that he cannot contact her to ensure both their safeties. They say goodbye, fondly.
As they carry the dead body into the woods, Novick and Pierce get a call from Jack. He intends to get Logan to confess what he has done. Jack will need twenty minutes to get to the retreat, and he asks Novick to find a way to stall Logan from leaving for Washington.
Karen lets Buchanan know that she's been summoned to Washington by the White House. Chloe asks for high clearance for a new employee with tech specialties -- her ex-husband, Morris.
Chloe interrupts Morris flirting with a female CTU staffer. She needs him to do a digital audio transfer.
Novick comes to the First Lady's room and tells her that Pierce is safe and that Jack wants to get Logan to confess. Novick asks Martha to detain Logan from leaving the retreat.
Jack pulls up to the field where Pierce is hiding. Pierce informs him that the President is not riding on Marine One to the airport, but is using a Navy helicopter instead. Jack asks Pierce to help get him on that chopper.
Logan is surprised when Martha comes to see him. She apologizes for the way she has acted and asks him to forgive her for the hurtful things she said. Martha tells him she still loves him. She asks him to stay at the retreat a little while longer so that they can have time alone. Logan is at first resistant, but Martha kisses him and seduces him to wait.
Jack and Pierce sneak inside the Secret Service outbuilding on the retreat grounds. The agent on guard is checking the helicopter because the Presidential departure is being delayed. Pierce asks how far Jack is willing to go to get Logan to confess. "As far as I have to," Jack says.