I haven't really thought through this as much as I should, as you will see by some of the holes in the theory. But I've tried to throw out a lot of ideas so that people can build on them/make them better. Please do so!
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Fact: Ben grew up on the Island during the Dharma days. Fact: Jack/Kate/Hurley/Sawyer/Juliet have all flashed back into the Dharma days. (Remember what Harper Stanhope said to Juliet - "you look just like her"; yeah, that's cuz she IS HER).
Therefore, since these people flashed back to the Dharma days, that means that Ben has known Jack/Kate/Sawyer/Hurley since he was a young boy, and therefore knew that they "had to" come back (i.e. so that they could fulfill their destiny and end up on the Island in the Island's past).
Why did Ben kill Locke? I think that learning that Jin had survived spooked the hell out of him.
If Ben grew up in the Dharma days, then he knows who among the Oceanic 815 survivors is "supposed" to be alive in the Dharma days. Jin wasn't one of those people (i.e. Ben has no recollection of Jin). So, the fact that John just confirmed that Jin is alive, plus the fact that Ben rightly assumes that everyone who was left behind flashed back to the Dharma time, means that Widmore has again 'changed the rules.'
Upon this realization, I think some of Ben's basic assumptions about his ability to control the Island, and his relationship with Locke (see immediately below), were changed.
--Ben/Locke relationship has changed--
I think Ben was being sincere (for once) when he told John in the hotel room that he was protecting the O6 and John so that John "could lead." This would make sense if Locke had previously led the Hostiles during the Dharma time, and/or if Locke is Jacob.
--Proposed Ben timeline--
Consider that it is possible (maybe even likely) that Ben's personal timeline looks something like this:
1) Ben arrives on Island as a boy;
2) Dharma, led by Widmore and a faction of the Others we saw in the 1950s, controls the Island;
3) the Hostiles, led by Richard and a faction of the Others who oppose Widmore, are out of power and fighting Dharma (who knows why);
4) Richard recruits Ben (recall the jungle scene in Man Behind the Curtain);
5) Sawyer/Jin/Juliet arrive, join Dharma (as we'll see in Lafleur);
6) a couple of years later *in Dharma days time* Jack/Kate/Hurley/Sayid? arrive, and join Dharma through their connection to Sawyer (who has now lived three years since he last saw them);
7) Locke and Ben arrives in the Dharma days time via the now-repaired Orchid vault (see # 17 below);
8) Ben finds the younger version of himself, who he tells everything he needs to know about the future to control everything that happens during his life (i.e., the "rules," or things that have to happen). the older Ben dies because of this (perhaps because he broke the basic f-ing laws of physics by talking to his past self) in front of his younger self, in a very 12 Monkeys-ish fashion;
9) younger Ben and Richard take orders from 2007-Jesus-Locke and carry out the Purge (do Jack/Kate/Hurley/Sawyer all die in the Purge??!?! that would be messed up), which also somehow results in Widmore getting booted off the Island;
10) Ben somehow takes power from Locke, who becomes Jacob, and is trapped by Ben by the circle of ash;
11) Ben rules the Others for a few years;
12) Locke crashes on the Island and slowly regains power from Ben;
13) Ben moves the Island;
14) Ben and the O6 get on the Ajira flight;
15) Kate/Jack/Hurley/Sayid (?) flash from the plane back onto the Island in the Dharma time;
16) the rest of the Ajira flight, including Lapidus, Sun, Ben and now resurrected Locke, crash on the Island in 2007;
17) Ben and Locke **repair the vault in the Orchid station** (who knows, maybe Caesar is a metallurgist?), thereby allowing them to travel back in time to the Dharma days without having to turn the wheel (which is probably why Widmore had it created in the first place);
--Locke-as-Jacob is backed up by the development of Locke's character--
When you look through the show's history, it seems more and more like Locke's story is about him being trapped or enslaved. Examples - 1) in Cabin Fever, when John was born, he was immediately locked in the incubator; 2) later in Cabin Fever, we see a teenage Locke trapped in a locker by some jocks; and 3) later in life, Locke's back is broken and he's trapped in a wheelchair. To me, a VERY logical (4) is when Locke becomes Jacob, and is trapped in the cabin by Ben (read: circle of ash).
Part of the Jeremy Bentham story was all about this part of Locke's personality. He HATES that he is not in control of his life. For all his talk of destiny, he only likes destiny when he feels that it is something that he is creating ("don't tell me what I can't do"). When he realized that Abbadon was a Widmore-plant, it really steamed him, because it made the one great thing he's ever had in his life just another example of how he is trapped.
--Putting it together--
When Ben arrived in the hotel room, he saw Locke about to kill himself and knew he had to stop him, so that Locke could fulfill his destiny and come to lead the Others (and eventually go on to order the Purge and perhaps later die and become Jacob; "you have too much work to do").
But when Ben learned that Jin was alive on the Island (probably assuming that Jin was also in the past/Dharma time), he realized that something had changed. This, combined with learning that Locke was about to make contact with Eloise Hawking, made it clear to him that he had to speed up the process of Locke "becoming" Jacob. That's why Ben said that he would "miss" Locke as he left the hotel room and Locke's dead body. Yes, he knew Locke would be resurrected on the Island, but he assumed it would be as Jacob, who he could control, as this is what had already happened in Ben's past (which is Locke's future).
What Ben does not realize, however, is that the course correction will bring Locke back to life *as* Locke, and Ben will need to convince Locke that he killed him "for his own good". If Locke believes him, he's again being manipulated, but destiny will be carried out. If he doesn't believe Ben, then he won't fulfill his destiny and Widmore will never get kicked off the Island during the Purge.
There's a war coming. It's been fought before, but now Widmore thinks he's got the most important piece on his side.Theory by Duuude
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Fact: Ben grew up on the Island during the Dharma days. Fact: Jack/Kate/Hurley/Sawyer/Juliet have all flashed back into the Dharma days. (Remember what Harper Stanhope said to Juliet - "you look just like her"; yeah, that's cuz she IS HER).
Therefore, since these people flashed back to the Dharma days, that means that Ben has known Jack/Kate/Sawyer/Hurley since he was a young boy, and therefore knew that they "had to" come back (i.e. so that they could fulfill their destiny and end up on the Island in the Island's past).
Why did Ben kill Locke? I think that learning that Jin had survived spooked the hell out of him.
If Ben grew up in the Dharma days, then he knows who among the Oceanic 815 survivors is "supposed" to be alive in the Dharma days. Jin wasn't one of those people (i.e. Ben has no recollection of Jin). So, the fact that John just confirmed that Jin is alive, plus the fact that Ben rightly assumes that everyone who was left behind flashed back to the Dharma time, means that Widmore has again 'changed the rules.'
Upon this realization, I think some of Ben's basic assumptions about his ability to control the Island, and his relationship with Locke (see immediately below), were changed.
--Ben/Locke relationship has changed--
I think Ben was being sincere (for once) when he told John in the hotel room that he was protecting the O6 and John so that John "could lead." This would make sense if Locke had previously led the Hostiles during the Dharma time, and/or if Locke is Jacob.
--Proposed Ben timeline--
Consider that it is possible (maybe even likely) that Ben's personal timeline looks something like this:
1) Ben arrives on Island as a boy;
2) Dharma, led by Widmore and a faction of the Others we saw in the 1950s, controls the Island;
3) the Hostiles, led by Richard and a faction of the Others who oppose Widmore, are out of power and fighting Dharma (who knows why);
4) Richard recruits Ben (recall the jungle scene in Man Behind the Curtain);
5) Sawyer/Jin/Juliet arrive, join Dharma (as we'll see in Lafleur);
6) a couple of years later *in Dharma days time* Jack/Kate/Hurley/Sayid? arrive, and join Dharma through their connection to Sawyer (who has now lived three years since he last saw them);
7) Locke and Ben arrives in the Dharma days time via the now-repaired Orchid vault (see # 17 below);
8) Ben finds the younger version of himself, who he tells everything he needs to know about the future to control everything that happens during his life (i.e., the "rules," or things that have to happen). the older Ben dies because of this (perhaps because he broke the basic f-ing laws of physics by talking to his past self) in front of his younger self, in a very 12 Monkeys-ish fashion;
9) younger Ben and Richard take orders from 2007-Jesus-Locke and carry out the Purge (do Jack/Kate/Hurley/Sawyer all die in the Purge??!?! that would be messed up), which also somehow results in Widmore getting booted off the Island;
10) Ben somehow takes power from Locke, who becomes Jacob, and is trapped by Ben by the circle of ash;
11) Ben rules the Others for a few years;
12) Locke crashes on the Island and slowly regains power from Ben;
13) Ben moves the Island;
14) Ben and the O6 get on the Ajira flight;
15) Kate/Jack/Hurley/Sayid (?) flash from the plane back onto the Island in the Dharma time;
16) the rest of the Ajira flight, including Lapidus, Sun, Ben and now resurrected Locke, crash on the Island in 2007;
17) Ben and Locke **repair the vault in the Orchid station** (who knows, maybe Caesar is a metallurgist?), thereby allowing them to travel back in time to the Dharma days without having to turn the wheel (which is probably why Widmore had it created in the first place);
--Locke-as-Jacob is backed up by the development of Locke's character--
When you look through the show's history, it seems more and more like Locke's story is about him being trapped or enslaved. Examples - 1) in Cabin Fever, when John was born, he was immediately locked in the incubator; 2) later in Cabin Fever, we see a teenage Locke trapped in a locker by some jocks; and 3) later in life, Locke's back is broken and he's trapped in a wheelchair. To me, a VERY logical (4) is when Locke becomes Jacob, and is trapped in the cabin by Ben (read: circle of ash).
Part of the Jeremy Bentham story was all about this part of Locke's personality. He HATES that he is not in control of his life. For all his talk of destiny, he only likes destiny when he feels that it is something that he is creating ("don't tell me what I can't do"). When he realized that Abbadon was a Widmore-plant, it really steamed him, because it made the one great thing he's ever had in his life just another example of how he is trapped.
--Putting it together--
When Ben arrived in the hotel room, he saw Locke about to kill himself and knew he had to stop him, so that Locke could fulfill his destiny and come to lead the Others (and eventually go on to order the Purge and perhaps later die and become Jacob; "you have too much work to do").
But when Ben learned that Jin was alive on the Island (probably assuming that Jin was also in the past/Dharma time), he realized that something had changed. This, combined with learning that Locke was about to make contact with Eloise Hawking, made it clear to him that he had to speed up the process of Locke "becoming" Jacob. That's why Ben said that he would "miss" Locke as he left the hotel room and Locke's dead body. Yes, he knew Locke would be resurrected on the Island, but he assumed it would be as Jacob, who he could control, as this is what had already happened in Ben's past (which is Locke's future).
What Ben does not realize, however, is that the course correction will bring Locke back to life *as* Locke, and Ben will need to convince Locke that he killed him "for his own good". If Locke believes him, he's again being manipulated, but destiny will be carried out. If he doesn't believe Ben, then he won't fulfill his destiny and Widmore will never get kicked off the Island during the Purge.
There's a war coming. It's been fought before, but now Widmore thinks he's got the most important piece on his side.Theory by Duuude