Everything Ben does is in the best interest of the Island and is to serve a greater good. While he has murdered people in cold blood, and is a pathological liar, it is all to protect the Island. Much like the wizard (the man behind the curtain) in "The Wizard of Oz," Ben is a liar but has good intentions for doing so. Any of his wrong deeds can be blamed on either the Island's will, or the greater good.
Benjamin Linus, like the rest of the people brought to the Island, is not a good or bad person; there is good and bad in everybody and it is the choices one makes that determines what kind of person they are.
When we see Ben with the Others under the leadership of Charles Widmore, he chooses not to kill the Rousseau's baby; he is also responsible for the death of his daughter because of his actions. Ben has made both good and bad choices in his past and continues to.
Ben would be technically good as Jacob had locked everyone who came to the Island into a cycle of life and death, prompting a rotation of candidates until Jacob's successor would be found. Everything that Ben did therefore safeguarded his position from being wrested from him by the whims of a quasi-immortal "God-king" and his actions also were for the best interests of the Island and his people.
He is good because he doesn't do anything out of cold blood he does it to better the Island or to protect it in the flash sideways, he decides not to move on meaning he feels bad for what he has done.
He is bad
Jacob and the Island gave Ben a tumor because he does things for his own personal gain and not the benefit of the Island.
Ben manipulates Sayid to kill people for his (Ben's) own gain. Everyone who Sayid killed could have prevented them from returning to the Island.
Ben manipulates everyone to benefit himself, not the Island. Ben was not supposed to return to the Island, but he tricked the O6 into returning, not for the gain of the Island, but because he knew they would be the only way he could selfishly get back.
Ben always has a ulterior motive for his actions, usually inconsistent with the lies he uses to justify his actions, meaning the use of the excuse that he is protecting the Island could be false to justify himself.
When Ben took Locke to see Jacob, he actually took him to the cabin where Nemesis lived. Ben has always followed Nemesis instead of Jacob.
This doesn't necessarily make Ben bad. It just means that he's a pawn like almost everyone else. He didn't knowingly follow the Nemesis. If he had, Fake Locke would've just been able to tell Ben exactly who he really was and what Ben had to do.
His killing of Jacob was pretty understandable, given that he felt Jacob was responsible for not preventing his daughter's death
After killing Jacob and learning all about Nemesis he still seeks to try turn the situation to his advantage. (Lying to Richard and the Others).
He has been bad, but since being manipulated by the Man in Black, Ben has realized the error of his ways and is seeking redemption (thus his comments about Locke and himself at Locke's grave).
Ben can summon the monster. He should go before Jacob to be judged, not the MIB.
Lost is never black and white. Neither Ben nor Widmore is purely bad or purely good.
What is good, what is bad? The question is somewhat irrelevant given that every main character seems to have some massive flaw. If it really mattered, then why are Kate and Sawyer, two murderers, considered important "good" guy characters in the show? "Good" and "Bad" never truly exists, only a grey scale in between. Ben is doing what he is meant to do, if he cannot change that, which we have been repeatedly told, then how can he be held accountable as bad or good. It is his fate, his destiny.
What about Jacob and Esau/MIB/Loops? Granted, ALMOST NOTHING is known about them, but they seem to be reasonably black and white.
Perhaps those two are just on a different level than "regular" people like Locke, Ben, Jack, etc...
The black/white theme throughout Lost pertains to everybody, including Ben; everyone has a 'scale' within themselves with both good and bad, it is the choices they make that determines what kind of individual they are.
Though Ben is a chronic liar, and it's never possible to be 100% sure about Ben, after the conclusion of season five it seems apparent that Ben is just as much out of the loop as many of the other characters. In all likelihood, he thinks what he's always done is what Jacob has asked, even if that wasn't actually the case.
He and Widmore are playing a game
Ben and Widmore, are both playing a game for control of the Island. This is supported by the fact that in "The Shape of Things to Come", Ben says that Widmore changed the rules. The "rules" are something that Ben and Widmore have agreed upon previously. This games resembles a chess game, in which the winner comes away with control of the Island. Supported by the idea that Ben called Alex a "pawn" to convince Keamy not to kill her.
"Changed the rules"
The Lost Universe has to conform to a set of rules and Widmore figured out how to change them.
Perhaps Widmore tells Ben that Ben himself changed the rules because as far as Widmore is concerned, Ben attacked first because of an above theory that Ben went back in time, killed all of the freighties in the jungle, or actually on the boat (as well as the doctor who suddenly washed up) and then the Monster took over to course correct time. So technically, Ben changed the rules first and that is what Widmore meant by saying that Ben was the one who did the changing. So Widmore is in fact correct in saying this according to a timeline. Maybe this is why Ben comes back so dirty, he's just cleaning up from Rambo mode.
Ben can't kill Widmore because the Island won't allow it, just like Michael couldn't kill himself. Hence, "We both know that I can't do that."
It would seem that there was an unspoken agreement to not make this personal or involving each parties direct relatives (Alex wasn't Ben's biological daughter, but he raised her as one and therefore should be counted as one). So when Martin killed Alex, he stepped past the boundary and therefore broke the "rules."
This seems consistent with Ben's emotional reaction. When Alex died, he didn't seem shocked in the sense that they did something that was impossible to do, but shocked in the sense that the Widmore people crossed a serious line that he genuinely did not expect them to cross. His rage and shock was more along the lines of "how dare they!" than "how could that be possible?"
The rules are simply the rules to the bet or the game that Ben and Widmore are playing. They are playing for the Island and pure glory over the other. The Island has its own mysteries as does the Dharma Initiative. Ben uses all he has learned about the island and the "science" behind it to help him win, while Widmore uses his money and violence. Who will win? Ben? Widmore? Some unnamed party? The Island?
The rules are actual, written rules that tell the Island who can die and who cannot. For example, it is written that Michael cannot die (as shown by his multiple suicide attempts) while other characters can. Ben was certain that his daughter could not be killed and was shocked that Widmore had changed the rules. These rules are either entered into the computer system on the Island or told to Jacob.
Unlikely. Time travel is hugely apparent now and when someone already has a destiny it is determined in stone. When someone travelled from the Island to the future and a so-called person was alive, they will be alive till then. That is... if the rules aren't changed and that points back to the Valenzetti Equation equation as the Island is a micro version of that of the whole world.
Ben will track down Penny who is somehow back together with Desmond. Ben will try to kill Penny but Desmond will kill him first. This is the "great thing" that he will do because Ben has been trying to cheat fate, which is emboided by Mrs. Hawking who told Desmond about the "great thing."
The great thing Desmond was born to do was to push the button. In fact, as Mrs Hawking said during Flashes Before Your Eyes it is the "only truly great thing [he] will ever do".
Ben and Widmore are playing to a formal set of rules, either dictated by themselves or an intermediary. The fact Sawyer, Locke, and Hurley were playing Risk during this episode is very important here, especially when you take into consideration the dialogue during that scene. This is important not only for the obvious correlation between this board game involving world domination and the apparent battle between Ben and Widmore, but Hurley says "can't believe you're just giving him Australia. Australia's the key to the whole game." My eyes went wide at that line.
In addition to whatever meaning "changing the rules" has for the story, it also is a production reference used as a joke - the producers had claimed in an interview that all flashforwards will be shown in chronological order. They *changed the rules* by breaking the promised order (Iraq is obviously before Berlin and the Seychelles) and they are admitting it!
Widmore "changed the rules" when he killed Alex. However the "rule" is not that you can't kill family members, children, whatever. The rule is you can't knowingly kill another's "constant". When Charles killed Ben's constant he "changed the rules".
After "Dead Is Dead", we have some sense of "the rules" for a leader of the Others--foremost, always act in the Island's best interests (meaning, among other things, never leave the Island [unless banished, in which case, never return] and abstain from fostering contradictory attachments [i.e., no fathering of children off-Island]). While Ben accused Widmore of breaking the rules by killing Alex, Ben ultimately accepted that it was actually his attachment to Alex that broke the rules.
Again we go to the archives of professional wrestling for the quotation. Ben will never move on. Because as Michael 'freebird' said: "Heaven don't want me, and Hell is afraid I'll take over. Ben wrote the rules and rewrites the rules at his whim. When Jacob says "and what about you". Ben knows exactly what Jacob means. The remark was meant for MiB. Jacob is telling MiB that killing Jacob was committing suicide. Ben was on the road to picking off Widmore, Jacob, MiB, one by one. He was stopped by Faraday or somebody else. he will teach Walt well because Ben wants another adversary. Beside Michael was his kind of guy.
Ben WILL move on. Just as Michael is not able to move on yet because he has not fully atoned for his sins, Ben can't for similiar reasons. This is the idea of purgatory that was alluded to when the whispers were explained. certain people can't pass on because they aren't "ready." All of the people in the church at the end had lived fruitful lives, and even those like Sayid who had killed were deemed to be "ready." The misconception is that if the smoke monster "judges" someone to be acceptable, this doesn't mean this person is ready to pass on to the afterlife.
Unlikely Charles and Ben were ever constants. Though never confirmed, it's far more likely that Ben's constant was his daughter, Alex.
There are "rules" that define their relationship. These are the rules of time-travel and course-correction ("The Shape of Things to Come") ("The Constant"). Figuratively (not literally), they can't kill each other, as they say in ("The Shape of Things to Come"). This is because if each of them does, then the killer loses his constant.
He knew that Locke would succeed him
Locke was always meant to go to the Island. When Locke didn't join the Mittelos group and go to the Island when he was 16, the Island was forced to find a substitute. Locke would have been 16 years old, from May 30, 1972 - May 29, 1973. Ben came to the Island sometime in 1973. The Island settled for Ben when it couldn't have Locke... and Ben knows it.
Ben is upset and shoots Locke when Locke hears Jacob in Jacob's cabin, because Ben had convinced himself that Locke could not be his successor.
Ben shoots Locke to test this. If he is the John Locke who traveled through time and spoke to Ethan and Richard, he can't die because he hasn't traveled through time yet.
Alternatively, Ben doesn't know that that it's impossible to change something that has already happened, and hopes to kill Locke to prevent him from becoming the new leader of the Others.
Presumably, Ethan would have told Ben about his encounter with Locke near the beachcraft. At the time, Locke told Ethan that Ben had appointed him as the new leader. Ben was probably quite curious to see who this person was when he arrived.
But the conversation we see between Daniel and Desmond outside the Swan, and Desmond's sudden memory of it three years later, would suggest that Ethan wouldn't have known he spoke to Locke until after the events of 'Because You Left', at which point he was already dead anyway. These things don't seem to be remembered retroactively, otherwise Desmond would have remembered who Daniel was as soon as he first met him.
Never supposed to be the leader of the Others
Ben was never supposed to be the leader of the Others. Jacob and the Island are able to cure cancer and heal many medical problems. However Ben was allowed to develop a tumor that would have killed him if Jack would not have arrived on the island and saved his life. He developed the tumor because he was being punished for taking a position without it being ordained for him.
Christian, who said he was speaking on Jacob's behalf, told Locke (in the FDW) that listening to Ben never got him anywhere. If Ben was truly the leader, then his requests would be considered trustworthy and the right decision.
Widmore was supposed to be the leader at the time of Ben's reign. Widmore claims that Ben 'stole' the Island from him and 'tricked' him into leaving.
In the time of the DHARMA Initiative, women did not have a problem giving birth on the Island. This problem arose after Ben took over leadership of the Others. The fertility problems are a side effect of his not being the true leader.
Ben appears to be able to control the smoke monster; however, when Locke asked Ben what the monster was, he told him he didn't know. Ben 'awoke' the monster but he only appeared to control. He actually told it to do what it would have done anyway.
Ben was able to gain the loyalty of Bonnie and Greta in the Looking Glass station to lie to the others about the station being flooded. He also gained the loyalty of Mikhail, who killed Bonnie and Greta at his orders. Before Bonnie died she told Charlie how to turn off the jamming devices. She defied Ben only after she realized he had betrayed her. When Ben asked Richard and the Others to stand up against Locke when he was beating Mikhail so that they could visit Jacob, nobody obeyed him. Similar to a king whose subjects only obey when they feel the demand is reasonable.
When looking at a character, especially one as dynamic and deep as Ben, you have to give the writers and the character himself a break. Sure he always has a plan, but there are too many people devoted to whatever the cause is that Ben's motive cannot be to become ruler supreme. He never shows signs of wanting to become the supreme ruler, in fact often showing signs that he is lonely, and that he never wanted this position in the first place. Working for the Island, he knows his work is never done, and having been such a clear devotee of what the Island is and what it stands for, it would be not just a strange move for his character to only be in it for the power, but a dumb move on the writers part too, bringing an incredibly multi-dimensional character deeply involved in the story down to the level of a one dimensional "fill in" if you will.
Ben is the pawn of Smokey/Jacob's nemesis. He was manipulated into becoming the leader of the Others, but was not Jacob's choice (visions of his mother indicating he was to join the others). He needed to be ready to kill Jacob when the time came. To have him initiated into the others required him to be fatally wounded. Which only happened due to the timey-wimey loop.
Ben was meant to be the leader of the Others, Locke wasn't. There's no evidence to suggest that Ben's visions of his mother had anything to do with Jacob's nemesis. Nemesis used the time-skips to manipulate Richard into thinking Locke was the future leader, then after he assumed Locke's form he manipulated Ben into killing Jacob. Since Locke wasn't supposed to be the leader, Ben was still Jacob's chosen leader when he entered the statue at the end of "The Incident, Part 1". This is backed up by the fact that Jacob was entirely respectful of Ben throughout their confrontation in the statue, even asking him if he liked the tapestry. "What about you?" was not a sign that Jacob had never chosen Ben, but a reminder that Ben had a choice to make and that the conflict he was involved in was bigger than him. As Eloise says, "it's bigger than all of us".
His off-Island pursuits
Ben has been preparing for a life off the Island. That is the reason for multiple passports and currencies hidden in his house. Ben always has a plan and would plan for living a life off the Island should that day come.
Ben was able to retrieve countless amounts of information on anyone he chose while living on the Island. After he moves the Island he is still able to find out a lot of information very quickly about Sayid, Nadia and Nadia's murderer.
You are trusting Ben too much. Perhaps like he was manipulating Kate with blood tests, he was also manipulating Sayid giving fake evidence. Ben has just as big of a motive as Widmore to make sure no one looks for the Island.
Jacob only wanted Locke to turn the FDW. Ben manipulated Locke because he wanted off the Island in order to find Widmore; and Penny, to avenge his daughter Alex's death. Ben knew that it was supposed to be Locke who turned the FDW but told Locke that he alone was the one capable of moving the Island.
Ben and Annie, Alex and pregnancies
Ben falls in love with Annie and they try to have a child. Annie is one of the first, if not the first woman to die on the Island because of the pregnancy problems. Her death leaves a deep impact on Ben.
"Evidence": In "The Man Behind the Curtain" Ben is seen holding the doll Annie gave him on his birthday many years ago. The writers also have stated that Annie will be very important in later storylines about Ben, even more important than the Island's volcano.
Ben's mother died when he was born and he had to pay for it his whole life through his father's treatment of him, which is why Annie's death during pregnancy has such an impact.
Annie's death is the final straw that causes Ben to really join the Hostiles/Others, and start the Purge.
Ben kidnaps the infant Alex, both amazed that a woman (Rousseau) has given birth on the Island without dying and glad that he finally has a child of his own.
Investigating the pregnancy issues is one of the major goals of the Others when Ben is their leader. That is why Juliet is brought there and she kept from going home until the mystery of the pregnancy issues is resolved, because Ben is determined to find out what is causing them.
Ben does not want Karl to get Alex pregnant because he does not want to lose his other most important woman in his life and he even goes so far as to lock Karl in and tries to brainwash him.
It is implied Annie left when the Island was evacuated just before The Incident (event). Annie never had Ben's child. Annie went on with her life and Ben was heartbroken.
Ben hates Jacob due to that Jacob is the reason that Ben's beloved one get killed during pregnancy.
Jacob did choose Ben
Richard was telling the truth in "Dead Is Dead." Jacob wanted Ben healed and he wanted him to lead the Others. Ben never lost favor with Jacob. It was MIB that gave him the tumor, in order to manipulate him against Jacob. Re-watch Ben's exchange with Jack in "The Cost Of Living." Ben: "Two Days I after I found out I had a tumor on my spine, a spinal surgeon fell out of the sky. If that's not proof of God, I don't know what is." Jacob brought Jack to the Island, so it's clear to me that Jacob wanted him to save Ben.
Jacob treats Ben respectfully during almost the entire scene in the statue. He patiently listens to Ben's monologue and he seems to have tears in his eyes. He knows that he caused Ben a lot of pain when he refused to meet with him, just like he knows his words will hurt Ben, but he knows it has to be done. Jacob wanted Ben to kill him, and he touches him when he dies.
I agree. Ben was chosen to kill Jacob by Jacob. Jacob is not trying to convince Ben to spare him but to kill him. When Jacob says "what about you?" It is almost as if he is answering the question "someone needs to kill Jacob, who is it going to be?" Jacob answers it "what about you?"... and Ben complies. It is also important that Ben has never had direct contact with Jacob so as not to arouse suspicions from MIB. It is also equalyy important that Ben has gone through hardships and tests of faith so as to provide a resonable background of resentment for Jacob. I have no idea what Jacob's ultimate purpose is, but I am pretty sure Jacob has somehow gotten around MIB's plan.
I believe that Jacob knew that only someone in his position (the protector) could kill MIB, but because of the rule Mother made, Jacob was not allowed to. MIB did not need to be killed until he found the loop hole that allowed him to embody Locke and there for in that moment in the Temple, knew that he needed to sacrifice himself to save the Island/possibly the world, and he needed someone to do it. He knew that Ben was the only one who had enough anger and resentment to go through with it and you can clearly see remorse on Jacob's face while Ben is asking him about why he had ignored Ben all those years, as well as for the nonchalant, knife-in-the-back comment "What ABOUT you?" that he knew would hurt Ben so much that it would drive him over the edge and kill Jacob. I also believe that Jacob possibly knew that Ben murdering him would bring about a change of heart in Ben - one that would ultimately lead to him becoming somewhat of a hero at the end of the show and prepare him for becoming the man he needed to be to become Hugo's "number 2".
Ben intended to be captured by Rousseau
Ben was lying when he told Locke he was on his way to kidnap him and accidentally stumbled into Rousseau's trap. He meant for it to happen all along - he had someone speak to Michael through the Swan's computer and pretend to be Walt, knowing that Michael would go in search of his son and find the decoy village; and before Ben left, he instructed his people to use Michael to lure Sawyer, Jack, Kate, and Hurley to them, and free Ben from the hatch in the process. Perhaps he planned to kill someone close to one of the aforementioned survivors himself when he escaped, so they would have a motivation to track him down, and he was pleasantly surprised when Michael took the task out of his hands and did it himself.
He also made the conscious decision to be shot with the arrow - he knew Rousseau was holding it, and that she would fire if he made an attempt to escape; and still he tried to run, knowing full well that if he were gravely wounded, Jack, as a devoted healer, would be far more willing to let his guard down, and that it would make his own identity - a hapless, confused victim - seem far more plausible.
Ben studied Henry Gale's background and knew intimate knowledge of him - too intimate just to have been gleaned in passing; he studied and rehearsed his character, because he knew he was going to play him. He intended to be captured as part of a reconnaissance and infiltration mission, knowing, as a result of Ethan's reports, that Rousseau would most likely tell Sayid of the Other she had trapped; and, once inside, he used his position to fill in the missing gaps that had emerged after the deaths of Ethan and Goodwin, and begin to manipulate the survivors, particularly Jack and Locke.
He believed that the two men he had previously sent to infiltrate them had failed, and so it was his responsibility, as leader, to do the job himself. He purposefully let the timer run down to zero during the lock-down, so that Locke would see the map on the blast door and save Ben the trouble of having to forcibly take him to the Barracks - Locke saw an unsolved mystery for himself, and Ben let him think it was his idea to try and solve it.
It's extremely unlikely that Ben, who knew the Island and its jungles better than anyone, and had personal experience with Rousseau, would be naive enough to fall over a trip wire and land himself in a net; and it's equally unlikely that he, himself, would make the journey to the hatch to try and kidnap Locke - it was the dirty work of a grunt, first of all, and even he wouldn't be so foolhardy as to think he could both take Locke down and carry him all the way back to the Barracks by himself. What other reason would he have for being alone in the middle of the jungle, so close to the Swan? He also wore a costume, indicating he was already planning to adopt a different persona from the moment he left the Barracks - if he were truly on his way to bring Locke back to the Barracks, Ben would have known he would have been far more likely to oblige if Ben had gone as himself, the leader of the Others paying a personal visit to the chosen one. The costume is also not his ragged Other clothes, which we see him wearing at the dock, and at the Pearl with Juliet - it's different, and it's specifically designed to look like something a man in a hot air balloon might have worn.
Furthermore, when Locke raised this same question to Ben - "did you get caught on purpose? You and your people have been here for God knows how long, and you got caught in a net..." - Ben skirted around the question and changed the subject; and when Colleen reported that Sayid had found the decoy village, Ben replied "good, it's what we wanted" - indicating that, in addition to him foreseeing everything else, he either also understood Sayid well enough to know he would not take well to being told he couldn't accompany the group, and would follow them anyway, or that he knew someone would soon stumble across it.
He knew what he was doing, and what the repercussions would be - Michael would find the decoy village and come back, he would be freed, and the chosen survivors would be taken to the Others of their own accord, no struggle necessary; and in the process, he would garner first-hand experience with the survivors and fill in all the blanks that Ethan and Goodwin's deaths had left. There was most likely also a contingency plan in place, such as waiting a week for word from him before sending help.
The fact that Ben told Michael "I'm not happy about the arrangement that was made with you" was most likely also a lie - perhaps because he knew Jack, Sawyer, Kate, and Hurley were listening, and wanted to keep the true nature of his imprisonment concealed, and perhaps because the sight of the leader begrudgingly adhering to the deal his people had made out of honour could win favour with them. This idea is supported by the fact that, when Juliet accompanies Ben to the Pearl to watch the survivors inside the Swan, she asks whether they are simply going to kidnap Jack, Sawyer, and Kate, to which Ben replies that "they need to come with us", and that Michael will make that happen - thus indicating that everything that went on to happen, from Michael being lured to the decoy village, to Ben's imprisonment, had been carefully planned by the latter.
Everything about what happened was too clean and perfect to have been anything other than one of Ben's plans - he knew what would happen, and even if certain aspects were unplanned mistakes, such as the survivors finding Gale's body and Ben not accounting for the note in his pocket, most if it was planned from the beginning. As Harper tells Juliet much later, when Ben finds himself imprisoned, it's because that's "exactly where he wants to be".
It's also worth noting that the corridor leading to Ben's bedroom is adorned with framed paintings of hot air balloons. Perhaps part of his desire to go undercover himself was an eagerness to play and inhabit that particular role out of a personal interest in hot air balloons, the one of the doomed pilot - as an experiment in manipulation and human psychology, and also for fun and curiosity.
The Annie doll is his Constant
The fact that he has kept the carved doll with him since childhood may very well be more than mere personal sentimentality - it could also very well be practicality. Realistically, it is the only small, portable object that he has continuously owned since he was ten years old, particularly as he came to the Island with very little - the books came later, the rabbits died, but the doll was there for over thirty years. And, as Daniel explained, a Constant has to be "something that you really, really care about".
That Ben carried it with him even to his mobile camp might also make a little more sense when considering this theory - certainly, the fact that it was his birthday and he held the only gift he had ever received close to him, and that he cared for Annie even after all these years, played a part, but Ben rarely did anything without ulterior motives, or owned anything for the sake of nostalgia and novelty alone; his home was cozy and well-decorated, filled with souvenirs from his travels, but everything most likely had a practical use as well, such as the painting concealing the safe and the bookshelf in front of the secret room.
He loved the doll and the comforting memories it conjured, but it was also a necessary object that needed to be carried wherever he went, for his own sake.
The idea that a Constant has to be a person was disproved at almost the same moment the very concept was introduced, when Desmond asks "can it be a person?" and Daniel replies "yeah, maybe" - meaning that he theorised that a Constant being an inanimate object was far more common than a living being, most likely because ensuring that an item would be guaranteed to exist in other times would be far easier than ensuring that a person was still alive and well.
Though it was explained that characters don't remember their interactions with time travelers in their own past until it happens in linear real-time, the two other significant occurrences - Daniel speaking to Desmond in the latter's past, and Jin spending time with Rousseau and her team - happened only for 30 seconds and a few hours, respectively. Three years is quite a different story; and, despite the fact that Richard explained that Ben wouldn't "remember any of this", this presumably referred simply to how he came to be wounded and how he was saved, and, thirty years later, Ben clearly has some memory of what occurred, as he refers to the Temple as the place "where the Island healed me", and recalls being brought there as a child - though, of course, there is the chance that he was simply told what had happened, and surmised the rest after he awoke in the Hostiles' camp.
Either way, it was never stated that the last three years of Ben's life were in any way wiped - and, though 30 seconds of Desmond's life is easily scrubbed clean by the Island, and Rousseau's memory went on to be mangled by mental illness and trauma anyway, it's a little harder to understand what precisely Ben remembered in the place of the people who played a constant role in the formative years of his life. It's possible that he remembered all the events, but that the faces of the people in his memories were blurry and foggy, and the details of their names and lives difficult to place, though he possibly remembered smaller features, such as feelings, voices, and smells.
It's equally possible that he remembered everything - and that, perhaps, the very reason the Island chose him to lead was because he was uniquely qualified to direct the Candidates' lives when next he met them.
He knew what was going to happen, but he didn't know how - he knew the end result, but he didn't know precisely how the pieces of their lives fit together to bring them to that point. Subsequently, everything he inflicted on the survivors was a desperate bid to keep them on the Island - because once he discovered who they were, he knew they had to stay, for any reason, and he was floundering blindly to make it happen. This, along with seeking to bolster the Others' numbers with stolen children as they can't give birth to their own, and his general desperation to keep the Island's location a secret from Widmore, explains his more inexplicable actions - such as why, precisely, he made everyone's lives so much more difficult and complicated than they had to be by terrorising and torturing the survivors, rather than simply offering help in exchange for surgery on his tumour, and then keeping them trapped on the Island once the operation had been completed; the reason being, he knew that this method would keep them occupied far longer: giving them problems to solve and mysteries to answer on their own would force them to remain on the Island for longer, and in a far simpler fashion, than they otherwise would have if he had had to put the effort into either finding a way to keep almost 50 people hostage, or killing the ones he didn't need.
Again, as he didn't know precisely how the core group would end up in the past, and we can assume he was acting without much, if any, guidance from either the Man in Black or Jacob through Richard, he was essentially playing a game of chess blind, and simply hoping the pieces somehow ended up where they needed to be. Everything ended up so cluttered and confusing because that's either precisely what he wanted - if the string was knotted, it would make it all the more difficult for the survivors to untangle themselves from it and escape the Island, and if they were occupying themselves with the obstacles he kept throwing at them, they weren't stopping to think about much else but basic survival - or because he really, truly was running blind and hoping for the best.
The only characters he shows a particular interest in, the only characters he keeps in captivity on Hydra Island, are the ones he met as a child - because he wants to know more about them and how they fit into his own story, and because he knows he has to keep them on the Island, no matter what. This is why he is so desperate to bring them back later - not only because they need to return for the Island's sake, but for his own: if they don't go back, if they don't play their roles in his own life, what happens to him? Devotion to the island and selfish self-preservation, in true Benjamin Linus style.
Certainly, a part of the reason Ben kidnapped them was because they were on Jacob's list, but Jack wasn't on the original list, and was only added by Ben so he could perform the surgery - and because he knew he was important both to the Island, and to himself.
He lets other characters die and leave the Island because he knows he didn't meet them as a child, and so they aren't supposed to stay there; he lets Michael leave because he knows that neither he nor Walt end up in the past, and he knows he is able to kill Locke - in that, he isn't breaking any rules by doing so - for the same reason. On that note, the reason he takes such an interest in Locke and his unique connection to the Island, despite obvious reasons such as jealousy and perhaps having been given snippets of information by Jacob or the Man in Black through Richard, is because he's incredibly curious as to how someone who seems so important doesn't end up with the others in the 1970s, and he wants to know why.
When Harper comments that she isn't surprised that Ben has taken such an interest in Juliet, because she "looks just like her", she isn't referring to his mother - she is referring to Juliet herself, though Harper herself doesn't realise the significance of this, and simply thinks Juliet bares a striking resemblance to the blonde woman from the 1970s that Ben has always been so fixated on. Juliet saved his life as a child, and, subsequently, he is obsessed with her, blending her into a revered childhood memory that's equal parts beautiful savior and mother.
When he tells Sayid that he is a killer, he is simply spouting back the words Sayid said to him before he shot him as a child - Ben has been shown to appreciate private in-jokes that no one else will understand, such as when he comments on the lack of Stephen King books during his captivity in the Swan, and he can't resist the irony.
In conclusion, he remembered all of them and everything that happened, even if he didn't know how it all came to be, and his actions from the very beginning were designed to keep the survivors on the Island and help bring about his own past - as well as the fact that he was just personally curious as to who these people he spent three years of his life were, thus explaining the reason he went to the trouble of being captured by them, just to spend time among them, and the reason he knew Locke was somehow unusual. He didn't know that anything from his childhood was out of place, that they shouldn't have been there, but once he sees their photographs in the files that Mikhail gathers, he recognises them, and knows they're important.
It's also possible that Richard, knowing they were time travelers, raised Ben in the knowledge that they would someday come back, and that he had to be ready for that day.
This theory also explains how Ben, after having just crashed back on the Island on flight 316, knew the survivors were trapped in 1977, despite never having been told so, and despite no one he was with knowing anything about it. Canonically, he knew about the Island's fragile relationship with time, and, after having watched them disappear before his eyes on the plane, he surmised that time had caught up to itself, that his present had caught up to his past, that this was the moment they found themselves in his childhood, and that Jin, Juliet, Sawyer, Daniel, and Miles must already have been there.
The fertility problems were punishment for Ben's leadership
The fact that women were unable to carry to term was not a result of the Incident, but rather a punishment inflicted on Ben by the Island. It disapproved of his style of leadership - namely the fact that he had disrupted and interfered with his people's ancient connection to the Island by moving them out of their spiritual home of the jungle and into the Barracks, that he was dishonest and kept secrets from them, and that he had altered and modernised their way of life, with the introduction of DHARMA technology, and effectively corrupted and diluted their sacred relationship with the Island when he was only trying to bring them into a new era and give them a better life - and sent the fertility problems not to harm the mothers themselves, but to punish Ben with the knowledge that they died because the Island was unhappy with him, and to create instability within the community.
It most likely wasn't punishment for his use of violence, as both Eloise and Widmore used brutality during their time as leaders, with the latter going so far as to order the execution of an infant, and it was most likely an accepted part of life; Ben brought sophistication and urbanity to the Others, but they were still fundamentally feral, and had only lived out of the jungle for around a decade.
It was punishment for taming and domesticating people that were supposed to be wild and free, for locking them up in little yellow houses and dressing them in ironed shirts and teaching them to use washing machines when they were supposed to be in the jungle, for cutting them off from their divine relationship with the Island and forcing them to listen to his will, and his will alone. They were not supposed to inhabit DHARMA stations and organise book clubs - they were supposed to protect and serve the Island, and Ben unintentionally obstructed their purpose. He was the most revolutionary leader in recent history, but the Island didn't want a revolution - it wanted stability and peace. As the Man in Black told Ben, when he was under the guise of Locke, relocating his people into houses "doesn't seem like something the Island would want".
There seemed to be no problem with pregnancies and birth during the latter stages of Widmore's leadership, as no one responded with any sort of shock upon seeing Alex when Ben brought her back with him as an infant, or hearing that Rousseau had successfully given birth on the Island.
When Locke joined the Others on their pilgrimage to the Temple, Richard lamented the fact that "Ben has been wasting our time with novelties like fertility problems". Why else would he devote so much time to such things, and with such manic obsession, unless he knew that it was his fault that his people were dying, and he felt guilty? The fact that Richard saw something odd with the leader trying to save the lives of the women under his care also indicates that it hadn't been the case during Widmore's reign - because the problem hadn't yet existed.
Claire was able to safely give birth to Aaron because the punishment only concerned those in Ben's care - and, as Claire was an outsider, she was exempt. All women who were not under Ben's rule, and who gave birth on the Island, would be able to safely deliver their baby with no adverse side effects for either them or their child, as the Island had no quarrel with them; Claire and Rousseau are both examples of this exclusion. Indeed, as Juliet and Ethan, with the exception of Claire, only studied women living under Ben's leadership, it's likely that other women do gain benefits from the Island, just as men experience an increase in sperm count.
As the leader was traditionally meant to have a close enough bond with their people so as to represent them as a whole, the Island sees the people as an extension of their leader, and punishes them for their sins accordingly when they can't punish the leader themselves. It was also the most effective way to discipline the leader - if their people were dying, and it was their fault, what wouldn't they do to help them?
First the Island sent Ben the fertility problems, as a warning - and when still he did nothing, because he didn't know what to do or why it was happening, it punished him again with a tumour on his spine.
It's also worth noting that Ben moving his people into the Barracks may very well have been the event that made Jacob cross his name out on the list of Candidates; considering that the majority of the viable Candidates left by season six had all committed murder, it most likely wasn't Ben's killing of his father.