As Ben runs from Ilana in the jungle, he finds the rifle that Locke told him would be leaning on a tree. In what could be Michael Emerson's best performance to date (though there are so many amazing ones), Ben tell's Ilana why he killed Jacob and about his choosing the island over Alex, leading to her death.
He asks her to let her go and join Locke and when she asks why, he says "Because he's the only one who'll have me." Ilana says "I'll have you," signaling some inkling forgiveness of Ben's murder of Jacob. He then follows her back towards the beach camp.