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I have always believed in Ben as having good intentions, even though he has not necessarily shown this or proven it through his actions, but he has always felt strongly in serving a higher purpose for a greater good (although that good is still relatively unclear). I feel like the "Dr. Linus" episode confirmed his ultimate path - his true destiny - to serve the best intentions of the island, to take the path of the good. He even said the only reason he would go to Fake Locke was because he was the only one who would accept him. He learned from Miles that Jacob did have some faith in him - that he hoped he was wrong about him right before he killed him. Ben's new "goodness" was also confirmed in the flashsideways, where instead of using his power to destroy another person (Principal Reynolds) he used it to help someone (Alex) achieve what they wanted most. He sacrificed his own desires by turning them into the desires of someone else.
The "sides" are starting to take clear form. Ben has chosen to fight for "Jacob's army", meaning those who are fighting for the sake of Jacob and to protect the island, which includes: Ilana, Sun, Frank, Miles, Jack, Hurley and Richard. However, unfortunately for Ben, right when he is taking a turn for the better, Widmore has arrived at the island, which will definitely cause turmoil and call into question once again both his morality and goodness.