Despite Jack's warnings, Locke and Kate go inside the hatch. When they disappear, Jack follows them to be confronted by a face from his past. Meanwhile, Shannon has a strange encounter with what might be Walt in the forest.
While trying to survive after the raft has been destroyed, Michael and Sawyer discover a new predator out in the ocean, while Jin is nowhere to be found.
Desmond explains to Locke, Jack, and Kate how he got to the island and the importance of entering a sequence of numbers into the old computer he uses. Jack does not believe him while Locke wants to take a leap of faith.
Hurley is given the tasks of taken the inventory of the hatch's food supply. Having previously lost his best friend because he suddenly became a 'have' rather than a 'have not' after winning the lottery, Hurley finds this task particularly stressful as he is worried that the other survivors will resent him for holding out.
Michael goes off alone into the jungle looking for Walt. Jin and the mysterious, but seemingly friendly, Mr. Eko, set out to find Michael before he is found by the dangerous "Others.
As the tail section survivors make their way across the island with Sawyer, Jin and Michael, Sawyer's infection takes a turn for the worse. When he passes out, Michael forces them to take him in a handcrafted stretcher, unwilling to leave him behind as Ana Lucia wishes.
The hellish first 48 days in the lives of the tail section survivors are revealed, culminating in the shooting death of Shannon by Ana Lucia.
As the two halves of the island collide, Ana Lucia explores her past as a Los Angeles cop shot in the line of duty; an incident which killed her unborn baby and led her to seek vengeance on the culprit.
Triggered by the sight of a horse in the jungle, Kate flashes back to the original crime of murdering her supposed stepfather that started her life on the run.
Mr. Eko flashes back on his violent youth and subsequent path to religion when he discovers the statue Charlie has been hiding comes from a failed drug run that he was involved with in Nigeria.
After taking a gun, knocking Locke out and locking him up with Jack in the bunker, Michael heads into the jungle to rescue Walt. Locke, Jack and Sawyer attempt to go after him as Jack rebuffs Kate's attempt to join.
Charlie begins having vivid religion-themed dreams that Aaron is in danger. So vivid, that he awakens with the baby in his arms with Hurley trying to snap him out of his trance.
When Sun gets hurt in a failed kidnapping attempt, the suspicion is that the Others have returned. With some help from Sawyer, Kate suspects that Ana Lucia might be responsible to garner support for raising an army.
When Rousseau leads Sayid to a mysterious captive in the jungle, he becomes determined to find out if he is one of the "Others" by ways of torture. He locks himself in the empty weapons cache with the help of Locke who changes the combination so Jack can't get in.
When Claire’s baby, Aaron, comes down with a mysterious illness, Rousseau shows up hinting that her missing two weeks may hold the key for a cure. She enlists Libby to hypnotize her to try and retrieve her memories and slowly they come back to her, remembering how Ethan kept her drugged and injected the baby with an unknown elixir.
When Sun discover's she is pregnant, she isn't sure about telling Jin when it is revealed through her flashbacks that Jin can't be the father. Henry Gale continues to play mind games with Jack and Locke and implies he may have sent Ana Lucia and crew into a trap.
When the hatch goes into a strange lockdown mode, Locke is trapped inside with Henry Gale. Locke releases him to help get the blast doors open and ends up getting his legs pinned under the doors.
As Libby starts helping Hurley work through his weight issues, he appears to be losing his mind. He starts seeing Dave, a figure from his stay at the mental institution who he apparently had imagined back then.
Bernard rallies some of the survivors into making an SOS sign on the beach but Rose opposes the idea. Through flashbacks it is revealed how they met. When Bernard proposed to her, he discovered she was dying of cancer and he was determined to find a cure for her.
Jack and Kate find an exhausted Michael in the forest and bring him back to the main camp. He tells them new information about The Others. Ana Lucia has sex with Sawyer in order to get her hands on a gun.
Eko, following dream visions, takes Locke to go into the jungle in search of a secret location that Eko believes holds the answers to the mysteries of the island.
While preparations are being made to bury Libby and Ana Lucia, a plan is made to end things once and for all...by Michael. Curiously, he only wants a specific five people to make the journey to attack The Others.
Jack, Sayid and Sawyer swim out to the sailboat to find a drunk Desmond sitting inside. In flashbacks we learn about Desmond: that he was dishonorably discharged from his regiment with the British military, that he loved a woman named Penny Widmore whose father did not approve of him, that he accepted a sailboat from a Libby and planned to use the sailboat to win the race that Penny's father runs.