In the Sideways world, Locke wakes up in the hospital to find Jack alongside him. The surgeon says Locke is a "candidate" for a special procedure and might be able to walk one day. But Locke wants no part of it, causing Jack to search for the reason behind his injury.
This journey includes Benard, who was Locke's dentist, who Jack also learns was on Oceanic 815 and who gives Jack the name "Anthony Cooper" as the person also in the accident with Locke. Jack tracks him down in a nursing home, where he runs into Helen, who was visiting Anthony. We see that he's also in a wheelchair and is a vegetable.
Back at the hospital, Claire visits and asks Jack why their dad left her a music box. He has no idea. He then finds Locke and asks again about the surgery. Locke tells him he got into the wheelchair because he took his dad up for his first flight as a pilot, and instantly crashed. He wants to remain in the wheelchair as punishment for what he did to the man he loved more than anyone in the world. Jack tries to give him a speech about letting go, but Locke isn't having it. He wheels himself away...
... and Jack calls out "I wish you believed me," words John had said on the island at one point and which he also uttered in his unconscious Sideways state earlier. These stop Locke for a moment, and then he continues on. On the way out of the hospital, he passes Jin.
BACK ON THE ISLAND...
Fake Locke and Jack break everyone out of the cages Widmore's people had placed them in, supposedly for their own protection. They make their way to the plane, but Fake Locke gets their first and presents the castaways with explosives. He says they were wired to the engine and they cannot fly because Widmore may have wired more and it isn't safe. Off to the subamarine!
Sawyer doesn't trust Fake Locke and tells Jack, who says he's remaining on the island, to push Locke into the water. As they near the sub, Jack obliges. Widmore's men shoot from the jungle and wound Kate, causing Jack to carry her into the sub. Everyone is now down there except Locke and Claire. It dives, and Jack discovers something in his backpack: the dynamite Locke had taken off the plane.
As Sawyer tries to disarm it, Jack realizes: Locke can't kill them. He's trying to make them kill themselves. But Sawyer won't take that chance, pulls out a wire and the timer speeds up. As his final act on life, Sayid tells Jack the location of Desmond and races off to explode and save his friends. But this detonation causes flooding on the sub, as well as chaos. Lapidus is knocked up. Sun gets trapped by numerous objects and then Sawyer gets knocked up. Hurley swims to safety with injured Kate and Jin insists that Jack save Sawyer.
We're treated to a heartbreaking scene between Sun and Jin, as they drown together on the sub. The episode ends with Hurley, Sawyer, Kate and Jack alive, back on the beack - and Locke walking away from Claire, likely heading for Desmond, saying he must finish what he started.