In Ben's only flashback episode, 3X20 "Man Behind the Curtain", after arriving on the Island as a boy, at night he sees his dead mother calling to him outside the Sonic Fence. He goes out there in the darkness and bumps into Richard Alpert dressed as a savage. He wants to join the Natives but Alpert says he'll have to be very patient for that. Cut to about 15 years later when Ben helps the Purge kill off Dharma.
Thanks for the update, I really, really don't remember that scene. I must have been in the bathroom or something.
So basically what this means is that Richard Alpert took advantage of psychotic kid to do his murdering for him. Nice.