Disclaimer: I don't own Lost or it's characters.
Ben always knew that one day, he would kill John Locke. Not because he hated him or some devious plan required him to or the urge was so strong. In fact, he had tried to turn it around several times, and he had always meant it. But deep, deep down, he had known that it was no use. Ben would kill him, someday, sometime and he would succeed.
In the beginning, John had just been a minor annoyance, like a small itch that would'nt go away. Locke himself may have doubted from time to time that he was special, but Ben never did. And Ben also knew that there could'nt be anyone more special on this Island than Ben himself (except Jacob, of course), exspecially not someone as clueless and unprepared as John Locke, who had just showed up and been perfect. Whereas he, Ben, had worked on everything, manouvered it all into place, so that he could be where he was now. And what had it brought him? A tumour on his spine and his daughter dead at his feet. Sometimes he felt sick with jealousy and bitterness.
The irony was, in another world, another life, he was sure that they could have been great friends. When he had first spoke to John, if he had'nt been a prisoner pretending to be someone else, he would have just thought: Finally someone I can talk to!
That's why he had'nt left him during the lockdown. People he found interesting enough to spent more than a few minutes with were rare. He'd also enjoyed manipulating him, he had to admit. But John had done a pretty well job getting under his skin, too. Every question he had asked after he joined his people seemed to be designed to point out Ben's own shortcomings and gaps in knowledge. That's why he had to go. Because Ben could'nt have it, someone draining away his power like that, someone he started to care about at that.
He'd shot John once and left him for dead and it did'nt work. After that he tried, he really tried, to change the enevitable. He'd meant every word he said to him down at the orchid. He was focused on his revenge on Charles Widmore, anyway.
But then, John had left the Island, too. And suddenly, Ben was right back where he started, all good intentions forgotten. He had been glad to see John again, shocked, as he had walked in on him trying to kill himself. He was speaking the truth when he said what he said to make him come down from the table.
Yet Ben knew the moment John abandoned his plan and thanked him tearfully that it still would'nt do. It had to stop.
As he'd strangled the person that probably meant the most to him after his daughter, he wished more than anything that he would live in another world.