Shannon's inhaler runs out and Boone believes Sawyer has the remaining three in his stash. When Sawyer refuses to give them up, Jack and Sayid resort to torturing Sawyer until he agrees to reveal the location of the inhalers. In flashback we hear Sawyer's story and find he is not who he says he is.

When the raft the survivors have been building mysteriously burns down, Michael is convinced that Jin is responsible for the sabotage, which only serves to escalate their rivalry. Meanwhile, Sun stuns her fellow survivors with a surprising revelation, and Boone gives Sayid a warning about his step-sister Shannon. Lastly, more details of Jin and Sun's troubled marriage are revealed through flashbacks.

Jack suspects foul play when Michael becomes violently ill while building the raft. The suspects include Sawyer and Kate, who compete for the last seat on the raft and do anything possible to prevent each other from getting it. Meanwhile, a secret from Kate's past is revealed to the other survivors on the island.

Jack makes a decision regarding Ben's offer. Sawyer's life is placed in danger when Pickett decides to make good on his threat. Locke discovers a hidden message that may help unlock the island's secrets. Kate recalls memories from the past, which caused her to make an important choice.

On the island, the Man in Black attempts to recruit Sawyer in his attempt to leave the island, while an impromptu funeral is held for the real Locke. In the flash sideways, Locke is fired from his job and becomes a substitute teacher.

Richard Alpert's back story is shown: In 1867, he is brought to the island on the Black Rock as a slave. He makes a deal with Jacob to be his representative in exchange for immortality. In the present day, Hurley convinces him to help the candidates replace Jacob and stop the Man in Black from leaving the Island.

Jacob and the Man in Black are revealed to be twin brothers. They are raised by a mysterious woman who is charged with protecting the island. As revenge for the murder of their adoptive mother (who killed their real mother), Jacob throws his brother into the source of electromagnetism after being made the island's guardian, which transforms the Man in Black into the smoke monster.