Here's my theory:
We've discussed the idea that island Ellie is actually Faraday's mom, Mrs. Hawking. I'm pretty sure that is the case. (We've also discussed the possibility that she is young Charles Widmore's girlfriend/wife. I think this is likely as well.)So ... crazy theory or logical LOST plot progression? You decide.
I think Faraday went a bit loopy after all the time travel stuff and seeing Charlotte as a child. He couldn't stop trying to find a way to fix things. So he defected to The Others to join his mother, who he knew would be there. Then he spent the next several years teaching her all she needs to know so that in the "future" she can send the O6 back to the island (like we saw her do earlier this season) and MAYBE even fix the timeline for everyone.