He remained, however, an expert manipulator, a liar and a murderer, and he served as a villain for much of the series; he was the main antagonist of both Seasons 2 and 3, and an anti-villain in later seasons.
Past on the Island
Ben came to the Island a polite, quiet eight-year-old, the son of an abusive DHARMA Initiative janitor. He met the island's natives, who healed him after a prisoner he freed (a time-travelling Sayid Jarrah) shot him, and he remained in touch as he grew and worked for the DHARMA Initiative. He drove his father out of the DHARMA facility on his birthday and assures his dad that this will be the last time he forgets his own son's birthday. He puts on a gas-mask and kills his father with poison gas, then returns to the DHARMA facility to see that everyone else is dead too. He later ousted and replaced their leader, Charles Widmore. As their new leader, Ben tried to solve the Island's pregnancy issues, and he raised an adoptive daughter named Alex as one of the Others.
In 2004, Ben developed cancer, but the crash of Oceanic Airlines Flight 815 brought a surgeon, Jack Shephard. After entering the survivors' camp as a prisoner under the name Henry Gale, Ben was kidnapped by the survivors and locked in an empty gun locker at "the Swan" DHARMA station. He is interrogated by multiple characters and mentions to Sayid Jarrah that he buried "his wife" at the place where "his" hot-air balloon crashed. However, it seems that the buried body was Henry Gale's body, revealing Ben as one of the Others. Meanwhile, the Others were able to convince fellow 815 crash-survivor Micheal Dawson to let Ben go free and then he'll get his kidnapped son Walt back. Micheal returned to the Swan, killed Ana Lucia and "Libby" and let Ben escape from the Swan. Micheal was then meant to lead four 815 survivors to the Others in exchange for a boat off the Island. He did so and Ben took the prisoners away to prison cells.
Ben was revealed to have a tumor in his spine and Jack would have to get rid of it, but it seems that Jack wasn't willing to do this. He did do it (after forcing the Others to let Kate Austen and James "Sawyer" Ford out of prison or else Ben dies) in the end and left him a cripple in a wheelchair. John Locke later came to the Others' camp to rescue Jack and took Alex hostage so that Ben would allow it. He tells an Other to get "the man from Tallahassee", which Locke assumed to be a code at first, but dismisses so he could tell Ben his plan; destroy the Others' submarine because if he left, he would be a cripple again as it was before the crash of 815. He did blow up the submarine and is taken by Ben to see his father Anthony Cooper tied up. Ben insisted to Locke that Cooper would have to die before Locke could "join" them in anything.
Ben later got Juliet Burke to be a spy for him at the camp of the 815 survivors so they could determine who was pregnant among them and then kidnap the suspects. Locke got Sawyer to kill Cooper and then went to Ben to tell him that he did it, denying that Sawyer was even there. Locke convinced Ben to take him to see Jacob, who is apparently not someone "you just go and see". At Jacob's apparent home, Locke sees that Jacob isn't there and Ben was crazy. However, this was because Jacob could turn invisible. The cabin starts shaking and a fire starts from Jacob being angry at Ben and Locke leaves, convinced that Ben was crazy. Then, Ben takes Locke to the grave of all who worked for the DHARMA Initiative and shoots Locke, leaving him to die in the grave with all the skeletons.
He then went away with Alex to go stop the 815ers from reaching a radio tower to disable Daniel Rousseau's looping distress signal, since he had now learned from his minion Mikhail that a helicopter pilot named Naomi was on the Island now. Ben feared that the people from the freighter Naomi came from were intending to do evil things, so he went off to try and convince Jack to not call the freighter with Naomi's satellite phone. He was taken prisoner by the 815ers and dragged off to Daniel's radio tower. Alex also reunited with Daniel, who was revealed before to be her daughter. Ben would then proceed to get Mikhail to go down to a DHARMA station called the "Looking Glass" and prevent the signal emitting from it to be disabled by Charlie Pace and Desmond Hume. This failed, as Charlie got in contact with Desmond's former lover Penelope "Penny" Widmore and found out that the freighter wasn't hers.
Ben was still a prisoner by the time Season 4 began. Here, Ben was convinced that the people on that freighter were bad guys who were going to kill everyone on the Island. He soon found out that the freighter (called the Kahana) was sent by an enemy of his named Charles Widmore, who had actually gotten a fake plane into the Pacific Ocean so that the world wouldn't learn of the Island. Given that John Locke was in a wheelchair when the crash happened and now he could walk, along with another 815er named Rose having cancer that the Island has now cured, that would definitely be able to convince Widmore to do evil things to the Island. But first, his goal was to take revenge on Ben and torture him for replacing him as leader of the Others.
When Jack and Locke's argument over whether or not the people on the freighter were good or evil, they split up, with Locke taking Ben with him to the Others' housing area called (by the DHARMA Initiative) the Barracks, where Season 3 flashbacks showed that Ben had betrayed the Initiative and used poisonous gas to kill his father and everyone from DHARMA who dared to step foot on his Island. Freighter representatives Miles Straume and Daniel Faraday came to the Island on a helicopter with help from Frank Lapidus (the original pilot of Oceanic 815) and Jack convinced them to take Sayid and Desmond to the Kahana, hoping that they would learn if the Kahana was good or evil.
Later on, Ben states that he has a spy on the boat, whose alias was Kevin Johnson, and worked as a janitor. Sayid and Desmond discovered that Kevin was actually an alias created by Ben to be used by Micheal Dawson, who sought to make up for betraying the 815ers in Season 2. A mercenary from the freighter known as the Kahana named Martin Keamy arrives on the Island with several other mercenaries, sent by Widmore to kill Ben and destroy the Island. Upon arrival, they killed Other member and Alex's lover Karl and Daniel Rousseau and took Alex prisoner. Keamy took Alex to the Barracks, knowing about the dangerous "electric" fence that surrounded it to keep Jacob's nemesis away.
Alex sent a warning signal to the Barracks and Ben showed a secret passageway to escape from the villains, who had now killed 3 people and blew up Claire Littleton's abode. She survived this and Keamy executed Alex when Ben refused to listen to him. Before, Miles had asked that Ben give him $3.2 million dollars in exchange for a lie to be told to the Kahana stating that Ben already died. As revenge, Ben summoned Jacob's nemesis (the Smoke Monster) to the Barracks and makes it kill all the mercenaries, yet by some miracle Keamy doesn't die. Ben and Locke go to find Jacob and learn what they should do next; move the Island. To do so, Ben and Locke, accompanied by Hurley, go to a DHARMA station called the Orchid, which had access to a wheel they could turn to move the Island. At the Orchid, Ben told Locke instructions on what to do, since it was now time for Ben to trick Keamy into his own death.
He turns himself over to Keamy and gets him into a fight against Sayid, and gets Keamy shot by Richard Alpert. Now that this was supposedly done, Ben told Kate and Sayid to leave the Island now on the helicopter, then goes back to the Orchid. At the Orchid, Ben and Locke enter a station made for electromagnetic experimentation and Ben puts a series of metal objects inside "the Vault", despite an orientation film explicitly saying to not put metal objects inside. Keamy comes in, surviving with bullet-proof armor, and reveals a heart-monitor that will trigger a series of explosives at the ship if his heart stops beating. Ben stabs him to death and ends up destroying the ship, but he didn't care anymore. He put on a winter coat and told Locke that he leads the Others now, since if you move the Island, you can't come back. He blows a hole in the other side of the Vault, climbs into it and enters a frozen room with a giant spinning wheel. Ben says "I hope you're happy now, Jacob", turns the wheel and makes the Island vanish into the space-time continuum. At the end of the episode, Ben appears to Jack on the mainland in a morgue and tells him that they all need to come back to the Island; Kate, Hurley, everyone who left. They'll also need to bring along the body of John Locke as well.
Note: Not all of the events described in this paragraph are arranged in chronological order.
Before Ben managed to find Jack at the morgue at the end of Season 4, he is shown to have been teleported into the Sahara desert after he managed to move the Island. He manages to get to civilization after being found by a traveler with a camel. Through callous manipulation, Ben manages to track down Locke, killing Widmore's henchman Matthew Abaddon while Locke fled. After some time, he manages to find Locke in a hotel room, trying to hang himself. He talks him out of doing it, only to strangle Locke to death with the wire himself. He ditches the scene after cleaning off his fingerprints from the room, leaving it so that it appeared that Locke hung himself. He also sends men to Kate's house, where he has been raising Aaron, to take her blood and determine if she really is his mother; she fled with Aaron and met up at a dock an night-time later. Ben himself manages to convince Sayid to bring down Charles Widmore's vast empire, which leads him to Hurley at the mental institution he was sent to. He manages to break into Widmore's penthouse at some point, where he tells him that he'll kill his daughter as revenge for sending Keamy to kill him, which resulted in Alex's death.
Trying to make good on his promise, Ben finds Desmond with Widmore's daughter Penny and tries to shoot her dead, but Desmond fends him off. After this, Ben realizes that Jack is also needed for their return to the Island to happen, so he finds him breaking into a morgue and convinces him to take Locke's body away. They drive away in a van with it, later stashing it in a hotel room. Eventually, he manages to bring all of the Oceanic Six to a pier to discuss the Island, and he reveals that he sent the strangers to Kate's house. Sun held a gun at Ben, blaming him for killing Jin, but he said that he could prove that he's alive on the Island. He takes everyone to the elderly Hawkins, who is from the Island. Hawkins explains how the Island's disappearance happened, and how they must go back to save everyone that was left behind there. Despite some resistance, Ben manages to convince everyone to board a plane called Ajira Airways 316, piloted by Frank Lapidus. After flying close enough to the Island's general vicinity, a white light shines over the plane and the sound of an electromagnetic event could be heard. Once the light and the sound ceased, Ben, Sun, passenger Ilyana and a few other people from Ilyana's strange group remained, while Jack, Kate, Hurley and Sayid were gone. Frank was forced to make the plane land on Hydra Island.
Now back on the Island with Sun, Ilyana and the returning Miles Straume, Ben found himself confronted by Locke, which made no sense, since the Island cannot bring people back from the dead. Sun also grew suspicious of Locke. Ben and Sun later found a photograph of the 1977 DHARMA Initiative staff, which included Sawyer, Juliet and Jin, in addition to Jack, Kate, Hurley and Sayid, meaning that they were teleported to the 1970's when they disappeared from the plane earlier. Some time afterwards, Ben, still feeling horrible for Alex's death, goes to a cave to confront the Smoke Monster, and waited to be judged for his many crimes against the Island and the 815ers. There, the monster judged him for Alex's death, telling him to obey Locke's every command. Some time later, Locke leads the Others and Ilyana's group across to the Island, seeking to find Jacob and hopefully figure out the true reason behind everything that he's done to them since their arrival on the Island (and even before). During this time, Ben questions Locke's motives, and he reveals that he wants Ben to kill Jacob, which he decides that he'll do.
They all arrive outside of a shattered Egyptian statue remain (the foot of a statue) that Jacob lived in. Ben and Locke go inside to face their enemy, while outside, the Others figure out Locke's deception; he is not really Locke at all, but is actually the Smoke Monster taking his form, as the coffin of the real Locke still contains his body. The whole reason that "Locke" brought Ben out here was to have him kill Jacob, as he can't do it himself. Inside the statue, meanwhile, Ben stands face-to-face with Jacob, dressed in white and surrounded by tapestries that he made. Ben tells Jacob that all of the bad things that he has done in his life was to win Jacob's favor, but even though he did everything he asked, Jacob never showed himself; he confesses that he killed Locke because he was jealous of him for being favored by Jacob (like Moses, as Ben put it). Ben asks Jacob "What about me?", and Jacob coldly-replies "What about you?"; Ben, enraged, stabs Jacob twice and steps away while "Locke" kicks Jacob's body into a burning fire to be incinerated.
Ben left the statue to tell Richard Alpert to meet "Locke" inside, but is then shown the corpse of Locke that had been found among the wreckage of Ajira Airways Flight 316. In utter confusion, Ben enters the statue again and watches the monster in Smoke Monster form kill several guys who were brought to the Island by Ajira 316 to guard Jacob. The monster appears as Locke and apologizes to Ben for making him "see [him] like that". After the Smoke Monster leaves to recruit more people for the coming war with Jack and the other "candidates" that Jacob chose to replace him as protector of the Island, Ben finds himself attending an improvised funeral for Locke, apologizing for killing him. After arriving at a hidden temple populated by a separate group of Others, Ben finds Sayid after he killed two of their leaders, and manages to survive the Smoke Monster's subsequent assault on the temple. While the Monster recruits more of the temple's population, Ben goes with Ilyana and Miles, and Miles reads Jacob's last thoughts and learns that Ben is his killer. Ben apologizes to Ilyana for killing Jacob. They take Ben to the beach and force him to dig his own grave, but the Smoke Monster arrives and saves him, and convinces Ben to accompany him on his mission to leave the Island forever. However, Ben stays with the 316ers for the time being.
Charles Widmore later arrives on the Island with some henchmen and they set up a sonar fence to keep the Smoke Monster away from Hydra Island, where they set up shop. Widmore arrived at Ben's home back at the Barracks, where Ben and the Smoke Monster found him. After Widmore divulges some secrets to the Smoek Monster about the Island for fear of Penny's safety, Ben shot Widmore dead and sided with the Monster. However, he secretly kept a walkie-talkie so he could talk to Miles and Richard and update them on his status. While they spoke, the Smoke Monster told Ben that he wants to use Desmond to sink the Island to the bottom of the sea, allowing him to reach civilization at last. The Monster took Desmond out of a well he'd thrown him in and goes with Ben to the Heart of the Island, where they were intercepted by Jack and Kate. Jack, Desmond and the Monster went to the Heart, where Desmond unplugged the "core" stone within, causing the Island to start falling apart. Ben found himself pinned under a tree, but was saved by Miles and Richard, who took him back to Hydra Island to board Ajira Flight 316 and finally leave the Island behind forever. While everyone else fled, Jack and Kate manage to kill the Smoke Monster at last, and Ben chose to stay behind to help Hurley, the new protector of the Island, run things as his "number 2". They found Desmond and saved him, and Jack managed to plug the stone core back into place, saving the Island.
Meanwhile, in the "flash-sideways" timeline, Ben was portrayed as a teacher of European history at a school run by a man who doesn't care much for it. After death, Ben was a teacher of his previous 'daughter', Alex. As his acquaintances from the Island moved on, he chose to stay behind to work out his issues.