After the events at the Pala Ferry, Season 3 picks up with Jack, Kate and Sawyer being held prisoner by the Others on another Island. The Others as a group are revealed to be less omnipotent as first thought, wearing normal clothes and having many resources on the island, including electricity, running water and a large supply of food and weapons. Jack is held in an aquarium where he meets Juliet, an Other. Sawyer, in a cage, meets Karl in the cage opposite; but soon, Karl is moved elsewhere and replaced with Kate. She and Sawyer are forced to do hard labor with the rest of The Others. Ben promises Jack safe passage off the island if he complies to do what they need him to do.
Sayid, Sun and Jin begin to worry when Jack and his group aren't contacting them, so Sayid sets a trap. However, The Others board the Elizabeth using the submarine and steal it on Ben's orders, but not without a casualty. Sun fatally wounds Colleen, who is shipped back. Jack is forced to operate on her but is unable to save her, to the distress of her husband. Pickett beats Sawyer, and Kate confesses that she loves him.
After the Hatch implodes, Desmond is sent back into 1996 with Penny in London. Dismissing the recent events as a broken memory, he continues on with his life, failing to secure a job at Widmore Industries and earn Charles Widmore's respect. Desmond sees Charlie on the street, and his memories of the future return, causing him to seek help, to no avail; he instead comes across Ms. Hawking, who seems to have knowledge of future events and tells him about the universe's way of "course-correcting". Desmond breaks up with Penny, realizing there's no way to run away from his destiny to crash on the island, and suffers a blow to the head which causes him to be sent back to the present (on the island).
Desmond meets Hurley, who realizes he can see flashes of future events. Locke wakes up mute, returns to camp and has a vision of the late Boone who leads him through a surreal airport, eventually telling him he needs to save Eko. Along with Charlie, they rescue a severely injured Eko from a polar bear in its cave. When they return, the news has spread of Jack, Kate and Sawyer's capture by The Others and Michael's betrayal; the camp is in uproar particularly Nikki and Paulo. Locke vows to save their friends, but they must first wait for Sayid to return with the boat.
Jack soon discovers that he's there to operate on Ben's spinal tumor and Juliet surreptitiously asks him to kill Ben during the surgery, bringing their power struggle to Jack's attention. Back at the beach camp, when Sayid, Sun and Jin return without the boat, Locke plans to contact the Others via the computer in the Pearl so they can rescue their captives. Eko's condition worsens, and he crawls away in the night towards the Beechcraft. Locke and Sayid lead a group to the Pearl, track and find Eko there, and see a glimpse of one of the Others on the TV screen. Eko becomes the Monster's second victim, and they bury him in the jungle. Locke sees a hidden message on Eko's stick telling him to head north.
Alex warns Kate that Pickett plans to kill Sawyer, to avenge his wife's death. Juliet, on Ben's orders, brings Kate to plead with Jack to do the surgery, however he does not comply, thinking Kate has been "turned" by them by using Sawyer's life as leverage. Kate and Sawyer consummate their relationship in the cage, thinking it's Sawyer's last day alive. Jack sees them and grows jealous, and finally agrees to do the surgery, where he holds Ben's life ransom for Kate and Sawyer's freedom. The two fight for freedom, and run from Pickett, but they come across Alex who bargains with them - they rescue Karl from brainwashing - in return for a boat. Ben asks Juliet to help Kate and Sawyer escape in return for safe passage off of the island and also so Jack will stitch his bleeding kidney. Juliet kills Pickett, who was about to kill Sawyer. Kate, Sawyer and Karl sail to the main island. Juliet is then incarcerated for killing one of their own, but Jack bargains with Ben to commute her sentence of execution. The Others, with Jack in tow, head for the Barracks on the main island.
Kate and Sawyer return to the beach, but the latter stays behind while Kate, Sayid and Locke seek Rousseau's help in the jungle. The four leave and head north to rescue the still-captive Jack. Desmond tells Charlie the grave news that he's going to die after seeing him struck by lightning and drowning while saving Claire. In an effort to cheer Charlie up, Hurley fixes a newly found DHARMA Van and they take a joyride. Later, Claire concocts an impressive plan of capturing a seabird and attaching a rescue message. Later, two survivors are found apparently dead, but they are really paralyzed and ultimately buried alive. In response to this, Hurley cons Sawyer into leadership to calm the survivors after the recent traumatic events.
While heading northwards, Kate, Sayid, Locke and Rousseau discover the Flame and its inhabitant, who claims to be the last surviving member of the DHARMA Initiative. Sayid discovers otherwise and they find Bea Klugh hiding in the basement - both of them members of the Others. Mikhail kills Bea to avoid betraying their secrets, and the castaways take Mikhail prisoner. A day later, they come across the sonar fence, and Locke pushes Mikhail within its range to protect his secret of being paralyzed. They scale the fence using a branch and infiltrate the Barracks, however Jack has already made his decision to leave the island. Kate and Sayid are held prisoner, however Locke sneaks into Ben's house and is manipulated into destroying the submarine, which Jack and Juliet were going to use to leave the island. Ben then takes Locke to see his father, whom they've also taken hostage.
The Others vacate the Barracks, while Locke joins them. Kate then wakes in the jungle handcuffed to Juliet, and they make their way back to the Barracks while being chased and scanned by the Monster. Juliet reveals her deception to Kate by showing her the key, in an effort to win her trust. They reunite with Jack and Sayid, and then head back to the beach. The survivors are initially very distrustful of Juliet, but when Claire falls dangerously ill, Juliet reveals that she's got the medical skills to save her, and after picking up the tools, she does so. Jack's trust of Juliet creates a rift between him and the rest of the survivors at first, but for now they trust his judgment. However, when Juliet takes the pregnant Sun to the Staff to give her an ultrasound, it appears she is working as a mole for Ben, though her true feelings may lie with the survivors. Juliet eventually tells Jack about Ben's plan in private, and the fact that Sun will die in two months if she doesn't leave the island, and they begin to create a plan to combat the Others once and for all.
Desmond sees a flash of someone parachuting onto the island, leading Charlie, Hurley and Jin towards the visitor. Desmond believes it's Penny here to rescue them, and is initially willing to let Charlie die in hopes of reuniting with his ex-fiancee. Instead, as Desmond lets Charlie live, Naomi appears, not Penny. Mikhail, seemingly alive, stumbles upon the group and in return for his freedom, he stitches the injured parachutist. When Naomi wakes, she tells Hurley that the wreckage of Oceanic Flight 815 has already been found with no survivors. When they return to camp, they hide Naomi from Jack and Juliet because they don't trust them, and at first bring only Sayid in to question her. Naomi claims to have been hired by Penny Widmore to find Desmond and consequently rescue him. Eventually, the survivors hold a meeting in the evening when Jack and Juliet go missing to discuss the recent developments, as a freighter is anchored 80 miles offshore which holds potential rescue.
The Others reach the Ruins, where Locke's father is held prisoner. Ben tells Locke of his plan to kidnap the pregnant women from the survivors camp. Locke steals Juliet's Dictaphone tape, and Ben ridicules him in front of the rest of the Others by revealing he is unable to kill his father, showing he isn't ready to make a full commitment to their group. However, Richard, another "Other", provides Locke with a candidate who might commit the deed - Sawyer. After the Others break camp, Locke returns to camp and secretly leads Sawyer away, telling him Ben is captive in the Black Rock. Instead, he meets Anthony Cooper and realizes he is the man who destroyed his life, and consequently quenches his thirst for revenge by killing him as predicted by Richard. Locke gives Sawyer the tape and he heads back to the beach. Locke, however, returns to the Others and demands to see Jacob. Ben, initially doubtful, eventually complies even to the disagreement of the rest of the Others. In spite of the return of Mikhail, who brings information on Naomi, who could pose a threat, Ben leads Locke to see his leader, and the latter - whom only Ben can see - pleads Locke for help. Enraged with jealousy, Ben shoots Locke and leaves him for dead at the Mass Grave.
Sawyer returns to the beach with Juliet's tape as proof that she's a mole. Naomi is revealed to the rest of the survivors and they discuss the situation. Jack and Juliet return, claiming that Juliet has turned against the Others and is willing to help. In the morning, Jack leads a selection of the survivors to Danielle and here he explains his plan to combat the Others with dynamite. The survivors load the tents with dynamite, but Karl returns from the other side of the island with a message from Alex that Ben has decided to move up the raid. Jack leads the survivors to safety at the radio tower, as Charlie swims down to the Looking Glass to turn off the blocking signal so Naomi's satellite phone can call the freighter, willingly going to his death.
Sayid, Jin and Bernard stay behind to blow up the tents, but are captured by Tom and Ryan. Bonnie radios Ben and Richard about Charlie's arrival and Juliet's betrayal, so he sends Mikhail to sort them out. Ben realizes Alex has also betrayed them due to the survivors' knowledge of the raid coming early, and he decides to intercept Jack to tell him of the impending threat from the freighter. Jack doesn't believe him, so Ben demands they hand over the phone; since he doesn't comply, Ben radios Tom to execute Sayid, Jin and Bernard, and he seemingly shoots the three of them. Jack beats Ben and takes him prisoner, and Alex is reunited with her mother after 16 years. Locke, about to commit suicide in the mass grave, sees an apparition of Walt, telling him Naomi and the freighter are here to kill them all.
Mikhail, following orders, kills Greta and Bonnie, however is shot himself by Desmond. Sawyer, Juliet and Hurley head back to the beach to help the shooters, and they discover that they are alive. Tom believes Ben has lost his mind for keeping them alive. They fight the remaining Others and rescue Sayid, Jin and Bernard. Inside the Looking Glass, Charlie gains the code to the jamming equipment from Bonnie before she dies and disables it. However, he talks to Penny for a fleeting moment, but Mikhail detonates a grenade in the water and the room begins to flood. Charlie writes on his hand "Not Penny's Boat" in order to show Desmond that Naomi was lying after all, before drowning. Jack and the survivors reach the radio tower and Naomi calls for help. Locke appears and throws a knife in her back, threatens and warns Jack that calling the freighter is going to cause disastrous results, however he doesn't believe him. Jack calls the freighter anyway and Minkowski tells him they're on their way. The survivors celebrate, with rescue seemingly at hand.
Many of the character's lives continue to be explored in flashbacks, and they are detailed here in order:
- Jack Shephard is a spinal surgeon living in Los Angeles, who suffers from obsessive issues concerning the knowledge of his ex-wife's new boyfriend, and he seeks to "find himself" in Thailand, coming across Achara, a woman with a gift.
- Sun Kwon is a housewife from Korea, and commits an affair with Jae Lee. However, she also deals with blackmail from Jin's mother.
- Jin Kwon is a hit man working for Paik Heavy Industries, and he deals with having to kill a particular Jae Lee.
- John Locke was part of a commune, and when he contacts his father for the third time, he pushes Locke out of a window and he falls 8 stories, which paralyzes him from the waist down.
- James "Sawyer" Ford spends time in prison after conning Cassidy, and he discovers he has a daughter.
- Eko Tunde deals with the loss of his brother in Nigeria.
- Kate Austen is a fugitive from the law, and she contacts her mother to find out why she gave her up. Later, she falls in love and marries a police officer.
- Juliet Burke is a fertility doctor who managed to impregnate her sister, who was ravaged by chemotherapy. Juliet was contacted by Richard, a representative of Mittelos Bioscience to help with pregnancy issues on the island.
- Desmond Hume was a young monk at a Scottish Monastery, believing God had bigger plans for him than his marriage with Ruth. However, Desmond meets Penny.
- Hugo "Hurley" Reyes deals with the return of his father.
- Claire Littleton at a young age, was a victim of a car crash where her mother entered a comatose state ever since. Through this event, she met her father for the first time.
- Sayid Jarrah is incarcerated in Paris for revenge for torturing a past victim.
- Nikki Fernandez and Paulo were a couple from Sydney who stole a producer's diamonds.
- Ben Linus was a DHARMA Initiative workman who killed his father and the rest of the Initiative in the Purge and since became leader of the Others and only known contact of Jacob.
- Charlie Pace is a rock star based in Great Britain. He recalls the five greatest moments of his life.
Note 1: In "Through the Looking Glass, Part 1", Jack's first flashforward was featured.