Flash-sideways timeline (2004)
Just out of surgery, John Locke comes to, with his surgeon, Jack Shephard at his side. John recognizes his surgeon and Jack explains that they met after the flight from Sydney. Jack explains that John was in a car accident and that while he operated he found that John might be a candidate for a new surgical treatment to repair his pre-existing paralysis. Locke immediately and firmly refuses the offer. John's fiancée, Helen Norwood arrives and thanks Jack for saving him.
Jack enters a room where Dr Bernard Nadler is shaping a teeth mold. Jack asks to see a patient file. He explains that he is John Locke's surgeon and he believes Nadler did emergency oral surgery on Locke about three years previously. He is trying to find out how Locke was hurt. Nadler asks what is Jack's interest in Locke. Jack starts to explain that he met Locke after a flight back from Australia. Bernard immediately interrupts saying "Oceanic 815". He explains that he was seated across the aisle from Jack on that flight and teases him about flirting with his wife, Rose. He calls it "pretty weird". Bernard refuses to breach confidentiality but writes down the name "Anthony Cooper" and says this man was brought in with John Locke three years ago. As they part he says that he hopes Jack will find what he is looking for.
Jack goes to the Palms Nursing Home to see Anthony Cooper. Helen arrives. She asks that Jack let it go, that John doesn't want the operation and that it should be enough that he saved John's life. Jack says it's not enough. They go to see Cooper. He appears to be in a vegetative state. Helen reveals that he is John's father.
Jack is at Locke's bedside. Locke stirs and while still asleep says "Push the button, I wish you had believed me." Jack looks up and sees Claire arrive. They go to the cafeteria where Jack selects an Apollo bar from the self-serve machine. Claire says that the lawyer told her that her father especially wanted her to have the inlaid music box that she shows Jack. Jack says he doesn't know the meaning of the bequest. He tells Claire that their father drank himself to death in Sydney and that the airline has lost the body. Claire says that she just flew in from Sydney. Jack is befuddled when he realizes that Claire was also on Oceanic 815. They open the music box. "Catch A Falling Star" plays as their faces reflect in the mirror inside the lid. He offers Claire to come and stay at his flat. He says to Claire that they are not strangers, they are family.
Locke is being wheeled out of the hospital by an orderly. He passes Jin, who is on his way into a hospital room carrying yellow flowers. Locke tells the orderly he is being met by his fiancee Helen, and that he can push himself because he's had a lot of practice. Jack approaches Locke in the hall to say goodbye. Locke thanks him. Jack tells him that he went to see his father so that he could find out why he doesn't want the surgery. Visibly shaken by this intrusion into his privacy, Locke tells Jack the accident that paralyzed him and made his father vegetative was a plane crash. He explains he had just qualified for his pilot's license and begged his father to be his first passenger and although his father was frightened of flying he had convinced him to come because he told his father that he could trust him. He says he doesn't know what he did wrong but that it was his fault. Jack reminds Locke of their previous conversation where Locke helped him through the realization of his father's absence. Jack tells Locke that he must now also realize his father is gone, and that punishing himself won't bring him back. He says that "what happened, happened", and that Locke can let it go. Jack says it's not easy and he doesn't know how to let go either, and he hopes that Locke could "go first". Locke laughs nervously and says goodbye. As he wheels away, Jack calls after him, "I can help you, John. I wish you believed me." Locke pauses for a moment, then leaves.
Original timeline (2007)
Jack revives and finds himself in a dinghy. Sayid is nearby and welcomes Jack to Hydra Island.
At Hydra Station Sawyer, Hurley, Kate, Claire, Sun, Jin and Frank are led into the animal cages. Sawyer refuses to go in and seizes a rifle from Seamus. Charles Widmore arrives and grabs Kate and threatens to kill her but when Sawyer calls his bluff, Widmore says that he has a list of names - Ford, the Kwons and Reyes but not Kate Austin. He says it doesn't matter to him whether she lives or dies. Against Kate's remonstrances Sawyer gives up the gun and they are all taken into the cages.
Widmore says to Sawyer that although he won't believe it, he is doing this for Sawyer's own good. Widmore checks with his men whether the fence is live yet, and when he's told that it will be an hour he says to work faster because "he's coming".
On the beach Sayid explains to Jack that Widmore attacked with mortars and that Locke had saved Jack. He says that the rest of Locke's group scattered into the Jungle and that it is "just the three of us now". "Locke" arrives and announces that Jack's friends have been seized by Widmore and that he now wants to rescue them. Jack asks why Widmore would capture them and "Locke" replies sarcastically that he would ask but he doesn't think Widmore will talk to him. He suggests they break them out, run for the plane and be off the island before Widmore knows what is happening. Jack says that they are not his people and that he is not leaving the Island. "Locke" says that he hopes Jack will change his mind about that but in the meantime he needs Jack to get his friends to trust him. "Locke" says that Jack can trust him because he could kill Jack and his friends but he hasn't, that he saved Jack's life and now he wants to save Jack's friends too.
Sawyer and Kate pace anxiously in the cage. Kate says that Widmore wouldn't have "taken her" - she call Sawyer "James". Sawyer explains that Kate's name was crossed out in the cave that he saw and so it is right, he doesn't need her. Jin tells Sun about seeing their beautiful daughter in a photo on Sun's camera. Sun gives Jin back his wedding ring.
Suddenly the power generator dies and the smoke monster appears and kills Widmore's men. Seamus falls near the cages and Kate tries to reach the keys while Frank kicks at the gate. Jack arrives and opens the gate with the keys and frees the group. They trek to the plane. Kate asks Jack whether he is coming with them now. Jack says he will help get them on the plane but will not join them because he is "not meant to go". Sayid arrives and says they need to go because Locke is waiting.
"Locke" strides up to the plane. The guards shoot at him to no effect. He breaks the neck of one of them and shoots the other. Taking the dead man's watch he goes into the plane and finds wiring leading to a pack of C4 explosives. The Losties arrive and find the dead men. "Locke" emerges from the plane and says he killed the men but that Widmore knew that would happen otherwise he wouldn't have removed his "little fences". He explains that Widmore wants them all together in a confined space so that he can kill them all. He shows them the C4 he found and says that their new plan to leave means taking the submarine. Hurley interrupts in an aside, saying that Alpert said Locke is not meant to leave the island. Sawyer cuts him off pointing out that Alpert is not here. He thanks "Locke" for twice saving them and that says that he was wrong about "Locke." "Locke" says that the sub will be heavily defended and that they will need everyone. Jack says he'll help, but he is not going to leave with them.
As they leave Claire apologizes to "Locke" who says he understands. Sawyer whispers to Jack that he doesn't trust Locke one bit and asks Jack to make sure Locke doesn't get on the sub.
The group arrives at the dock. There is no sign that the sub is protected at all. Sawyer gives instructions particularly that Jack and "Locke" watch their backs and be last to go to the dock. When Sawyer, Sun, Frank, Jin and Hurley go to the dock there is no resistance. Sawyer opens the Sub's hatch and goes aboard. The group overpower the crew and Sawyer orders the Captain to "fire this thing up."
Kate, Claire and Sayid follow to head on-board. "Locke" gives Jack one of the back packs and they follow. On the dock "Locke" asks Jack to reconsider his decision, explaining that whoever told Jack to stay had no idea what they were talking about. Jack turns and says "John Locke told me I needed to stay" and pushes "Locke" off the dock and into the water. Kate looks around and as she asks what just happened a shot hits her in the shoulder. Widmore's team are firing at them. As Jack carries Kate on board followed by Sayid, "Locke" climbs onto the dock and shoots three of Widmore's men. Below Jack asks Hurley for a first aid kit so he can treat Kate. Sawyer goes above. Claire and "Locke" continue the firefight with Widmore's men. As Sawyer looks out of the hatch, "Locke" runs toward him. Sawyer closes the hatch leaving "Locke" and Claire outside. Sawyer uses the intercom to tell Frank to get the Captain to dive. Claire sees the sub leave and as she runs to it "Locke" restrains her with a look of satisfaction as he replies: "Trust me, you don't want to be on that sub."
Kate lies injured and realizes Claire has been left behind while Jack asks for his pack to get a shirt to apply to Kate's wound. He unzips the pack and realizes it is not his. He takes out the C4 wired to the watch "Locke" took from the dead man, the timer is counting down from 3 minutes 54 seconds. Jack says to them all that they did exactly what Locke wanted.
Jack yells that they must get to the surface and the captain is told to surface. Jack says to Sawyer that "Locke" wanted Sawyer to shut him out. Sawyer checks with Frank and discovers that they will take at least five minutes to surface. There is less than three minutes twenty seconds left on the timer. Sayid explains how to disarm the bomb but he has some doubt it will work. Sawyer goes to pull the wires but Jack stops him, saying that nothing is going to happen. He explains that Locke can't kill them, that this is exactly what he wanted, just as he had said of Widmore: "He wanted to get us all in the same place at the same time. A nice enclosed space where we had no hope of getting out of." He explains that Locke said he can't leave the Island without them but what is really the case is that he can't leave the island unless they are all dead. Jack guesses that "Locke" is trying to get them to kill each other - by pulling the wires from the C4.
He asks Sawyer why Locke would use a timer, why wouldn't he just throw the bomb into the sub. He pleads that they are going to be O.K., that they just have to trust him. Sawyer says he's sorry and pulls the wires. The timer stops at 1:31 and nothing happens. Then the timer re-starts and races down. Sayid tells Jack to listen carefully. Sayid tells Jack about Desmond's location, and says "Locke wants him dead, which means you are going to need him." Jack asks why Sayid is telling him this. Sayid says "Because its going to be you Jack." He picks up the C4 and runs down the passageway. The bomb explodes in his hands.
Water begins to flood the submarine. Frank gets up and looks at a bulkhead as it gives way and hits him with full force followed by gushing water. Jack finds Kate underwater and passes her to Hurley to take her out. Hurley asks about Sayid but Jack yells: "there is no Sayid." Sun is pinned against the side of the chamber by a metal cabinet. Jin, Sawyer and Jack struggle move the heavy cabinet but when they do, Sun is still trapped by a bar. Sawyer is hit on the head by a falling metal bar and knocked out. Jack grabs him. Jack still wants to help Jin free Sun but Jin says to go, that he should save Sawyer. He refuses the last oxygen bottle which Jack offers him and finally persuades Jack to leave. Jack has a long last look at Jin and Sun and swims out of the submarine with Sawyer.
Jin continues to try to free Sun despite her pleas for him to go. He holds her and says that he won't leave her. They embrace as water floods the submarine. The sub sinks and their hands drift apart in death.
Jack swims to the beach with Sawyer who coughs up some water and breathes. Hurley and Kate find them. Kate asks about Jin and Sun but Jack shakes his head. Hurley sobs and Kate cries. Jack walks to the sea and cries bitterly.
"Locke" and Claire are still at the pier. "Locke" says that the submarine has sunk. Claire is shocked that they are all dead but "Locke" says that not all of them are dead. He takes his pack and rifle and Claire asks where he is going. He replies: "To finish what I started."