Locke, Sayid, and Kate encounter the Others' homes for the first time and find Jack relatively happy amongst them. Jack and Juliet, whose relationship has advanced, have cut a deal with Ben to leave the island on the Others' submarine, but Locke blows it up. Ben reveals that he has Locke's father in captivity. In flashbacks, Locke's father pushes him out of a window, which paralyzes Locke.
Charlie tells Sun that he and Sawyer were behind her kidnapping attempt in the jungle. The survivors investigate the apparent deaths of Nikki and Paulo. Flashbacks feature past characters such as Shannon & Boone, and they show that Nikki and Paulo arguing over diamonds that they conned from a millionaire television executive. On the island, Nikki releases venomous spiders upon Paulo, but they are both bitten and stuck in an eight-hour paralysis. The survivors do not figure out that Nikki and Paulo are not dead, only paralyzed, and they accidentally bury them alive.
The Others and Locke leave the Others' homes, leaving behind Jack, Kate, Sayid and Juliet. It is shown the Others sonic barrier fences stop the smoke monster from going past them. Hurley cons Sawyer into making amends with his fellow castaways. Flashbacks show the steps Kate took to ultimately reunite with her mother, who did not want her.
"One of Us"
Jack, Sayid, Kate, and Juliet return from the Others' camp and because of his insistence to trust Juliet, the rest of the survivors question the motives of Jack. A mysterious illness strikes Claire, activated by an implant from the Others inside her. Juliet cares for her. Flashbacks show Juliet's time on the island. Juliet is kept on the island against her will and unable to save women who get pregnant on the island from death. Flashbacks also show Juliet conspiring with Ben to be a mole in the survivors' camp.
Juliet is put on trial for killing Pickett. With Jack and Ben's help, Juliet does not receive the death penalty. The Others and Jack begin their journey to the Others' homes, which are located on a different island. Flashbacks show Jack getting his tattoos during a strange vacation in Thailand.
"Tricia Tanaka Is Dead"
Kate and Sawyer return to the beach. Hurley finds an old, abandoned van in the jungle and drives it with Charlie, Sawyer and Jin. Kate, Sayid, and Locke venture off to rescue Jack. Flashbacks show Hurley's father returning home, after Hurley won the lottery.
Locke, Sayid and Kate investigate a Dharma communications station in the jungle and meet its inhabitant, Mikhail. As they are leaving the station, Locke blows it up. Sawyer competes in a ping-pong competition against Hurley to get back his belongings, but loses and has to go without calling people nicknames for a week. In flashbacks, Sayid meets one of his former torture victims in Paris.
Claire learns about Desmond's prophecy. She later ties a rescue message to a bird and releases it. Locke, Sayid, Kate and Danielle approach a sonic barrier fence protecting the home of the Others during their mission to rescue Jack. Locke shoves Mikhail, an Other whom they have captured as a hostage, into the fence and he dies. Locke, Sayid, and Kate climb over the fence without any problem. It is revealed in flashbacks that Claire shares her father with Jack. Claire meets her father for the first time after her mother goes into a vegetative state, as the result of a car accident with Claire.
Eko follows what appears to be his brother into the jungle. It turns out to be the smoke monster, which proceeds to kill Eko. Jack finds out that the reason he was captured was to operate on Ben's spinal tumor. Juliet conspires with Jack against Ben, telling him to kill Ben during surgery but to make it look like an accident. In flashbacks, Eko becomes a priest after Yemi is killed and Eko kills a few men to protect his town.
Kate and Sawyer show their feelings for each other by having sex. Pickett almost kills Sawyer when Jack stops Ben's surgery and threatens to kill Ben unless Kate and Sawyer are given time to escape. In flashbacks, Kate tries to have an ordinary life and get married, but ends up running away after confessing to her husband about her past.
"Not in Portland"
The teenage "Other" Alex supplies Kate and Sawyer with a catamaran to return to their island, but first she convinces them to help her rescue her boyfriend Karl from a room where he is being brainwashed by being forced to watch a video. Juliet kills Pickett, who is in pursuit of Kate and Sawyer. Jack finishes Ben's surgery. Flashbacks reveal that over three years prior to the crash, Juliet is a fertility doctor, and is able to make her sister fertile. Juliet is interviewed by Mittelos Bioscience.
"Flashes Before Your Eyes"
Charlie and Hurley attempt to get Desmond drunk so he will explain to them how he is able to see the future. An extended flashback reveals what happened to Desmond after the implosion of the hatch. Desmond relives a day of his life with Penny before coming to the island. He finds himself on the island again with the ability to see flashes of the future, most notably Charlie's approaching death.
Jack is imprisoned in the Hydra, a Dharma Initiative station, and interrogated by an Other named Juliet. Kate and Sawyer are kept in nearby cages. Sawyer tries to escape with a teenage Other named Karl, but they are caught. "Henry Gale", whose real name is Ben, is revealed to be the leader of the Others. In flashbacks, Jack obsessively tries to find out who his wife Sarah is having an affair with during his divorce settlement. Jack suspects his father and attacks him at an Alcoholics Anonymous meeting. Jack is arrested and bailed out by his wife.
"The Glass Ballerina"
Ben offers to take Jack off the island if he cooperates. Kate and Sawyer are let out to smash rocks and it is revealed that they are under video surveillance by Ben. On the sailboat, Sun, Jin and Sayid are ambushed by the Others. Sun shoots the Other Colleen and the boat is taken by the Others. Sun, Jin and Sayid make their way back to the survivors' camp. Flashbacks show Sun's father finding out about Sun's affair with Jae Lee. He orders Jin to kill Jae, but Jin threatens Jae instead, and Jae subsequently commits suicide.
Locke, Desmond, and Eko survive the implosion of the hatch. Locke sees a vision of Boone and goes with Charlie to save Eko from a polar bear. Hurley discovers that Desmond can see the future.
"Every Man for Himself"
Colleen dies and her husband Pickett takes out his anger by beating Sawyer. Sawyer is deceived into thinking that a pacemaker has been implanted in him and that his heart will explode if his heart rate exceeds 140 bpm. Ben reveals to Sawyer that trying to escape is futile because they are on a separate island off the coast of the island where the survivors' camp is. In flashbacks, Sawyer cons his way out of prison and finds out that he has a daughter. After claiming that he doesn't care about her, he anonymously gives a large sum of money to his daughter.
Mr. Eko and Locke find another Dharma station, which is monitoring the other stations via video surveillance. Meanwhile, Jack and the other survivors struggle with the deaths of the shooting victims in the hatch whilst trying to save Libby's life. In flashbacks, Eko investigates a miracle as a priest in Australia.
Michael convinces Jack, Kate, Sawyer and Hurley to help him rescue Walt. At the double funeral for Ana Lucia and Libby, Sayid tells Jack of his suspicion that Michael has been compromised by the Others. Flashbacks reveal Michael's time being held captive by the Others, during which he made a deal to first release Henry, and then trade Jack, Kate, Sawyer and Hurley for Walt. Sun spots a sailboat floating towards the beach.
"Live together, die alone"
In flashbacks, Desmond is shipwrecked on the island and subsequently lives in the hatch with a man named Kelvin, whom he later accidentally kills. Meanwhile, Michael leads Jack, Kate, Sawyer and Hurley to the Others. Henry, the apparent leader of the Others, releases Hurley, takes Jack, Kate, and Sawyer as prisoners, and allows Michael and Walt to leave the island on a boat. Desmond returns and realizes that he caused the crash of Flight 815 when he entered the numbers into the computer too late. Locke stops entering the numbers and traps himself, Mr. Eko, Charlie and Desmond inside the hatch, which implodes. In the epilogue, scientists working for Penelope Widmore locate the island.