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He eventually wanted control of the island. When he heard Eloise Hawking's name in "The life and death of Jeremy Bentham", he panicked (because he knew of her relationship with Charles Widmore) and killed John Locke. Any relation to Widmore he saw as a threat.Ben explains this to Flocke in 'Dead is Dead.' He said that John couldn't get the people to come back to the island, and his death would be the catalyst for this (which in fact, it was). However, it can be later seen in season 5 and 6 that Ben was actually jealous of Locke, because he was 'Special', whilst Ben was not, and John was destined to be the new leader of the others, perhaps even the 'new Jacob.' Ben, desperate to hold onto whatever power he had, eliminated the threat of John. In the end, nothing would bring back what mattered most to Ben: not his power, but Alex.overwelming emotion