The season premiered on February 2, 2010, with a double-length episode (two hours including commercials) preceded by a one-hour clip show, entitled "Lost: Final Chapter". The show continued from February 9 at its new timeslot of Tuesdays at 9 pm, with a total of 18 episodes airing in 16 broadcasts, ending with a two and a half hour, two-part series finale, the latter part of which aired Sunday, May 23, 2010. Additionally, the first hour of the premiere episode was screened to an estimated 15,000 fans on Waikiki Beach on January 30. In the following table, "Series #" refers to the episode's number in the overall series, whereas "Season #" refers to the episode's number in this particular season. "U.S. viewers in millions" refers to the number of Americans in millions who watched the episodes live or recorded them and watched them within seven days of broadcast.
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The sixth season followed two timelines, each an outcome of the explosion of a hydrogen bomb in the previous season finale. In the first timeline (referred to as "flash sideways"), Oceanic Flight 815 never crashes but lands with all leaving the airplane at Los Angeles LAX airport. In the second timeline, the remaining survivors return to the present day (on the Island) and must deal with the demise of "Jacob", whose death has been caused by the mysterious Man in Black, the Smoke Monster. According to show producer Damon Lindelof, the term "flash-sideways" was deliberately used instead of "alternate reality" because it might then imply "that one of them isn't real, or one of them is real and the other is the alternate to being real."
On the island, it is revealed that, long long ago, infant "Jacob" and his brother were stolen, from their birth mother, by a woman who raised them to become protectors of the island, after her. At the hidden center of the island, is a waterfall cave containing a bright power source. "Jacob" (with blond hair) and his brother (with black hair, symbolizing white and black) grow up with opposing viewpoints. "Jacob" stays loyal to his adoptive mother, but his brother joins with outsiders on the island. When the brother reveals that they have dug into the core of the island, tapping an underground power to escape, the mother hits the brother with a rock, and she destroys the people in their village. She then chooses "Jacob" to drink the water of immortality. His brother awakens to see the burned village, and seeking revenge, he finds and kills his adoptive mother. "Jacob" discovers her dead body, and in turn, throws his brother into the waterfall cave, transforming him into the black Smoke Monster.
Now centuries later, among the survivors, the Smoke Monster assumes the form of "John Locke", returned to the island in a coffin. This "Locke" had convinced "Ben" to enter the seaside cave and stab "Jacob", who fell into the fire and died. With many survivors believing that "Locke" has been resurrected, they follow him in various plans to leave the island. In one plan, they overthrow the guards at "Widmore's" submarine, and leave the island, unaware that a time bomb is inside the submarine. "Jack" (the doctor) discovers the time bomb, advising them not to disarm it while reasoning that the Smoke Monster cannot kill anyone directly. Instead, "Sawyer" (Ford) refuses to listen and pulls the bomb wires, which, instead, causes the bomb to count down faster. "Sayid" grabs the bomb and runs through the submarine, sacrificing himself to shield the others from the bomb blast. However, the bomb splits the submarine walls, and while sinking, "Sun-Hwa" is trapped in the wreckage, but "Jin" stays with her, vowing to never leave her side again, as they both die underwater.
"Jack" swims, with a breathing tube, to the surface and back to shore. He tells the rest that "Sun" and "Jin" did not escape. In anger, "Kate" vows to kill "John Locke", for what he has done to their friends. "Sayyid" (the Iraqi guard), "Richard", and "Miles" (son of the DHARMA leader) go to the other island to destroy the airplane. However, crossing at sea, they find the pilot adrift, who convinces them to repair the airplane to escape later.
The spirit of "Jacob" asks who among them would become Protector of the island, and "Jack" volunteers. At the waterfall cave, "Jack" drinks the water of immortality and returns to the group. "Jack" says they must meet with "Locke" and "Desmond" to settle the dispute and kill "Locke". The 2 groups meet on the hilltop, and just the 3 proceed toward the waterfall cave. There, "Desmond" descends on a rope into the cave, but pulls a rock from the bottom, which puts out the light of the power source. The island begins a series of earthquake tremors, to fall into the sea, with rocks tumbling into the water. "Locke" flees the area, now needing to get the sailboat to the other island: he has lost his immortality when the light source was put out. "Jack" chases him to the sea cliffs to stop him from leaving, and a long fight begins. "Locke" grabs a knife and stabs "Jack" in the side, then forces the knife up to "Jack's" neck. Before plunging the knife, a gunshot is heard: "Kate" as promised, has shot "Locke" (the Smoke Monster) in the back, and "Jack" pushes him off the sea cliff, to die on the rocks below.
"Jack" tells them he must return to the island core, as he promised Jacob, to restore the light at the waterfall cave. He instructs "Kate" to leave with "Sawyer" to get "Claire" into the airplane on the other island. "Kate" in turmoil kisses "Jack" goodbye, fearing it will be the last time. "Kate" and "Sawyer" jump into the sea and swim to the sailboat at anchor.
"Hurley" and "Ben" help "Jack" return to the waterfall cave. They lower "Jack" into the cave, where he revives and ties "Desmond" to the rope. "Jack" then puts the missing stone back into the floor, and restarts the light power source. When "Hurley" and "Ben" pull the rope, they find only "Desmond". They call below, but "Jack", overcome by the knife wound and rushing water, never answered, so they take "Desmond" away from the area. Some time later, Jack awakens, alone, outside the cave, as if lifted from the depth of the cave by an unseen force. Dazed, he wanders through the jungle, but he is losing strength. Just as with "Locke's" death, "Jack" also lost his immortality, and protection, at the first time the light source was put out. "Jack" falls to the ground, looking up to the blue sky. At that point, he sees "Kate's" plane flying far overhead, and then closes his eyes, for the last time.
Meanwhile, in the "flash-sideways" view of events, everyone has returned on Oceanic Flight 815, and all have resumed their original lives:
Soon after returning on Flight 815, "Desmond" has been tasked to ensure that bandmember "Charlie" stays sober to appear at a benefit concert for Charles Widmore. "Charlie" keeps talking about some imaginary, profound romance with a blonde girl, as if in some dream. Trying to rebel against "Desmond", he grabs the steering wheel, and the car goes into the harbor. Underwater, looking back inside the car to save "Charlie", he remembers seeing "" written on "Charlie's" hand, but not actually, then pulls him to the surface. They get rescued to the hospital, and Desmond asks, "Who is Penny?". Some memories come back, and Desmond begins to orchestrate a plan: at the school, he hits "John Locke" with his car, causing him to need surgery, led by "Jack Shephard" at the hospital. "Desmond" turns himself in to the police station for "Sawyer", who puts him in a jail cell near "Kate" and "Sayid".