On Jacob's orders, Hurley leads Jack to a lighthouse. Meanwhile, Claire questions an Other she has captured while tending to an injured Jin. In the flash sideways, Jack is a single father trying to bond with his son.
After recruiting Sayid to his cause, the Man in Black issues an ultimatum to the Others: either join him or die. Meanwhile, Kate is reunited with Claire. In the flash sideways, Sayid helps his brother, who is in debt to a loan shark.
Ilana discovers Ben killed Jacob, so she plans to kill him. Meanwhile, Jack, Hurley and a suicidal Richard visit the Black Rock. In the flash sideways, Ben, a high school teacher, tries to blackmail the school's principal.
The Man in Black sends Sawyer on a reconnaissance mission to Hydra Island, where he discovers that Charles Widmore has returned to the island with a team of scientists. In the flash sideways, Sawyer is a lonely cop who is still searching for the original Sawyer.
Two outcomes of the detonation of the nuclear bomb are presented. In the first, Flight 815 lands safely at LAX, where Kate escapes from the marshal and Jack learns that his father's body was lost in transit. In the second, the survivors return to the present day after Jacob's death; Juliet dies and Sayid is resurrected after being brought to the Others' temple. Also, the Man in Black, who is impersonating Locke, is revealed to be the Smoke Monster and kills several of Ilana's team from Flight 316.
"What Kate does"
When Sawyer escapes from the temple, Kate and Jin are sent to bring him back. Meanwhile, the Others determine Sayid is infected and attempt to poison him. In the flash sideways, Kate, still on the run, takes Claire to a hospital when she goes into labor.
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.
Upon learning that Penny did not send the freighter, the survivors of 815 split into two groups led by Jack and Locke. Meanwhile, Hurley and Claire struggle with the news of Charlie's death. In flashforwards, Hurley is revealed to be one of the "Oceanic Six"—a group of six survivors, including Jack and Kate, of the crash of 815 who have escaped the island.
A science team from the freighter flown via helicopter by pilot Frank arrives on the island. A single flashback for each of the freighter crew members introduces their backstories. The episode's final flashback focuses on the late Naomi, who meets with Abaddon to discuss the science team and pilot. The team consists of Daniel, a physicist; Miles, a medium; and Charlotte, an anthropologist.
Locke's group settles into the Barracks. Sayid makes a deal with Frank to leave the island, in exchange for freeing Charlotte. Sayid holds up his end of the deal; however, he obtains Charlotte by trading her for Miles. Frank, Sayid and Desmond leave the island for the freighter by helicopter. In flashforwards, Oceanic Six member Sayid works as an assassin for Ben.
Jack learns of the Others' plan to ambush the survivors and kidnap their pregnant women, and he comes up with a plan to kill the Others with dynamite. Desmond informs Charlie of another flash in which Claire and Aaron are saved as a result of Charlie swimming to an underwater Dharma station that is jamming all transmissions. In order for this to work, however, Charlie must die. Charlie understands his fate and successfully makes it possible for Sayid to send out a distress signal from Naomi’s satellite phone. Charlie writes down the five greatest moments of his life and gives them to Desmond to give to Claire.
"Through the Looking Glass"
In this double-length episode, Jack's plan to kill the Others backfires, and Sayid, Jin, and Bernard are held hostage by the Others at the beach. Led by Rousseau, the castaways travel to the radio tower to turn off Rousseau's transmission. Naomi makes contact with her boat, but is stabbed by Locke, who along with Ben, believes that the survivors are making a mistake. After successfully shutting down the jammer, Charlie makes contact with Penny Widmore in the underwater Dharma station and discovers that Naomi's boat has nothing to do with Penny, but Charlie drowns in the communications room when Mikhail detonates a hand grenade outside the porthole. Before drowning, Charlie warns Desmond by writing on his hand, "Not Penny's Boat." Sawyer, Juliet, and Hurley rescue the castaways at the beach. Instead of flashbacks, flashforwards feature Jack's miserable life after rescue from the island, culminating in a meeting with Kate in which Jack says that they weren't supposed to leave and must go back to the island.
Led by flashes, Desmond coaxes Charlie, Hurley and Jin on a trek across the jungle where they discover Naomi, a parachutist. Kate turns to Sawyer after seeing Jack alone with Juliet. Flashbacks show Desmond's time as a monk and his meeting Penny.
After learning that the Others' pregnant women died before giving birth on the island, Sun allows Juliet to examine her in the Dharma medical station. Juliet reports back to Ben. Desmond meets a living Mikhail in the jungle and allows him to help save the life of Naomi. Flashbacks show Sun being blackmailed by Jin's biological mother, whom Sun thought to be dead. Hurley learns that Oceanic flight 815 was "found" with "no survivors" from Naomi.
Flashbacks show Locke living with the Others, who have his father in captivity. In the present, Locke persuades Sawyer to go with him to the Black Rock to see Locke's father. Sawyer kills Locke's father who happens to be the original Sawyer.
"The Man Behind the Curtain"
Locke returns to the Others and Ben begrudgingly takes Locke to meet the Others' mysterious leader Jacob. Locke is unable to see Jacob, but can hear him, and because of this Ben shoots Locke and leaves him for dead. The survivors' mistrust of Jack peaks when Juliet is exposed as a mole; however, Juliet in turn reveals that she has been working with Jack against the Others. Flashbacks show when Ben first came to the island as a boy as part of the Dharma Initiative. Ben conspires with the Others (at least one of whom, Richard Alpert, does not age in the next thirty years) and kills most of Dharma.