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We find out that the Others live in a compound in an area of the island previously unseen. Ben, the leader, is known as Henry Gale to the beach survivors.
Jack, Kate and Sawyer are held under video surveillance on what we discover to be a second island about a half mile away.

Kate and Sawyer are forced to perform hard labor and Jack is interrogated by Juliet, an obstetrician who is plotting against Ben. Ben discloses his spinal tumor to Jack. Jack operates and, with Ben at his mercy, negotiates the release of Kate and Sawyer.

In an attempt to save Jack who is still held by the Others, Kate, Locke, Sayid and Rousseau rush to his rescue.

Along the way, Locke destroys the Flame, a Dharma station. We meet Mikhail, who is taken prisoner and is apparently killed by Locke.

They find a happy Jack, who is waiting for Ben to take him off the island. The submarine is destroyed by Locke, who now learns that Ben is holding his father, Anthony Cooper.

Locke leaves with the Others and Cooper while Jack returns to the beach with Juliet, Kate and Sayid.

Desmond has a vision involving Penny Widmore and being rescued. A parachutist named Naomi lands in the jungle and is injured. Naomi claims Penny hired her to find Desmond. She says that Oceanic flight 815 was found and everyone declared dead.

Ben tells Locke to kill Cooper. Locke cannot do this, but manipulates Sawyer into doing it after learning that Cooper was involved in the death of Sawyer’s parents. Locke sends Sawyer back to the beach with evidence revealing Juliet as a spy and news of an impending raid by the Others.

Ben tells Locke that he takes orders from someone named Jacob. Locke forces Ben to take him to see Jacob.

When they arrive, Ben speaks to an empty chair and as Locke turns to leave, he hears a voice say “Help me”.

Ben leads Locke to a mass grave, shoots him and leaves him for dead. When asked why he shot him, Ben replies “Because you heard him”.

Naomi has a satellite phone that links her to a ship, but the signal is jammed by an underwater Dharma station called the Looking Glass.

A three-part plan is devised in which:
Jack will lead the survivors to the radio tower.
Jin, Bernard, and Sayid will stay behind and detonate strategically-placed dynamite with gunfire, killing as many Others as possible.
Charlie and Desmond will go to the Looking Glass station and shut off Ben’s jamming signal. According to Desmond‘s vision, the mission will succeed but Charlie will die.

Locke, still alive and re-paralyzed is about to shoot himself. A vision of Walt tells him he can walk and he has work to do.

Ben intercepts Jack and the tower-bound group saying that Naomi is lying, and everyone will die if the call is made. Ben is taken captive by Jack.

Charlie is successful and disables the jammer.

Outside the station, Mikhail detonates a hand grenade and Charlie drowns. Before dying, Charlie shows Desmond his hand, on which is written “Not Penny’s Boat”.

Rousseau disables her S.O.S. call. Naomi calls the ship on the satellite phone, but Locke kills her and tells Jack they are meant to stay on the island.

Defiant, Jack speaks to the ship and rescue is on the way.