In the episode, flashbacks reveal how Desmond came to the island. In realtime, Desmond unintentionally returns to the beach and is enlisted by Locke to help him stop the button in the hatch from being pushed. Meanwhile, several castaways head off to rescue Michael's son, Walt, from the Others.
While at the funeral for Ana Lucia Cortez (Michelle Rodriguez) and Libby, a boat comes into view out at sea. Several castaways swim out to it and find a drunken Desmond piloting the boat. The next day, after Mr. Eko (Adewale Akinnuoye-Agbaje) prevents Locke from destroying the computer that controls the timer, Locke enlists Desmond's help in letting the timer run down to zero. Desmond hotwires the blast doors shut, locking Eko outside the computer room and Desmond and Locke inside of it. Eko, distraught, seeks Charlie Pace's (Dominic Monaghan) help. The two attempt to use dynamite to blow the blast door open, but the plan backfires, injuring both of them.
Meanwhile, Desmond and Locke discuss the purpose of the stations and discover that when Desmond accidentally allowed the timer to run out, the magnetic force pulled Oceanic Flight 815 toward the island, thus causing the crash. Locke continues to doubt that the timer has any meaning, but Desmond assures him that it is all real, as the timer passes zero, Desmond retrieves a failsafe key and crawls underneath the hatch to reach the system termination switch, and inserts the key. A shrill humming noise and violet-white light envelopes the entire island, causing the Oceanic 815 survivors and the Others alike on opposite sides of the island to bend in apparent pain. That night, Charlie is the only person to return from the hatch; the whereabouts of Desmond, Eko, and Locke are not revealed. Charlie reconnects with Claire Littleton (Emilie de Ravin), and they kiss as they sit among their fellow plane survivors.
In present time, the survivors split up into two groups to head to the Others' camp. Michael Dawson (Harold Perrineau), Jack Shephard (Matthew Fox), Kate Austen, (Evangeline Lilly), James "Sawyer" Ford (Josh Holloway), and Hugo "Hurley" Reyes (Jorge Garcia) walk on land to the camp, bringing guns and ammunition with them. Meanwhile, Sayid Jarrah (Naveen Andrews), Sun-Hwa Kwon (Yunjin Kim), and Jin-Soo Kwon (Daniel Dae Kim) plan to use Desmond's sailboat to go by sea. Sayid plans to use black smoke as a signal, saying that "this time, they will know that we are coming", a reference to the attacks in the first season finale. When the boat reaches the Others' camp, Sayid finds it to be deserted. Meanwhile, Michael, Jack, Sawyer, Hurley and Kate engage in a gun battle with some Others that were following them, and Sawyer kills one. Jack confronts Michael about leading the group into a trap, and Michael confesses to the murders of Ana Lucia and Libby. They realize that Michael has led them to a location other than the beach, ruining their former plan to meet up with Sayid. They hear whispers, and suddenly Sawyer, Kate, and Jack are incapacitated by electric darts. The hostages, bound and gagged, are brought to a dock, where it appears that the Others are lead by Henry Gale (Michael Emerson). Gale keeps his bargain with Michael, returning his son, Walt Lloyd (Malcolm David Kelley), to him and giving them a boat, which Michael uses to get off the island. Hurley is then released and sent back to the other survivors with a message that they are to stay away from the Others' part of the island.
The scene shifts to what appears to be a cramped polar research station, where two men speaking Portuguese are playing chess. The game is interrupted by a beeping monitor, whose screen displays the message ">/ 7418880 Electromagnetic Anomaly Detected". One of the men makes a frantic phone call to Penelope Widmore, saying, "I think we've found it."
"Live Together, Die Alone" was the thirteenth episode of the series directed by Jack Bender. The episode was written by Damon Lindelof and Carlton Cuse, the ninth episode that the two had written together.
Due to being two hours long, more time went into shooting "Live Together, Die Alone" than most episodes. It was shot in 17 days by two separate crews. Several scenes had to be shortened or cut due to time constraints. One scene that was cut was: after it is revealed that Michael was a traitor, Sawyer wanted to go back to the camp, because he thought it would be stupid to keep following someone who lied to him. In the past, Lost has had an issue with spoilers being leaked from the set, so for the production of "Live Together, Die Alone", the crew took extra steps to ensure secrecy of pivotal scenes. Alex Petrovitch, who played Henrik, recalled that when auditioning for his part "names, places, and circumstances (of his scene) were shifted so that you couldn’t link the scene to the show." Even other cast members were not told about Petrovitch's scene. Another measure used by the cast and crew to limit the release of spoilers was calling the final scene by the code name "Challah" instead of referencing anything in the scene. However, the attempts to cover up the flashback scenes were less successful and a call sheet was leaked by Lost fan Ryan Ozawa onto the internet, detailing the full plotlines of Desmond's flashbacks, about a month before the episode aired. It is in this episode that it is revealed that Henry Gale is in fact the leader of the others. Originally Michael Emerson was slated to star in six episodes of Lost, according to Emerson, but after seeing him act, the producers thought that Henry might make a good villain.
"Live Together, Die Alone" received mostly positive reviews. IGN's Eric Goldman praised actor Henry Ian Cusick (Desmond Hume) for giving "a likable, sympathetic performance". Goldman went on to say that the episode "was a much better finale than last season, which aside from Walt's kidnapping", and that it contained one of the "more interesting flashbacks of the entire season". Entertainment Weekly writer Scott Brown described his viewing experience as "I was up, I was down, I was frustrated, I was thrilled, and finally I was...well, a bit numb." Brown criticized the way Charlie reacted to the hatch explosion, stating that he felt the writers were trying to "get us to hate Charlie".