This is the final paragraph in an interview with Lindelof and Kring(Heroes Creator) from the newest issue of Wizard(the comics magazine). This is the only thing having to due with what will happen in the show...everything else was just about writing and the friendship between the two writers.
Wizard: What can you guys tell us about how your shows will wrap up this season?
Lindelof: For us, I will say the construct of Season 3 started with our heroes victimized by this - at the time - unseen, malicious and malevolent force on the island of these "Other" people. By the end of the season, you will know a lot more about them and what they're doing there and why they've been preying on our guys.
There is going to be an epic confrontation between the two groups - for lack of a better word, a war - and that's where we are heading to in our season finale. Hopefully, people will be more satisfied than they were in previous seasons - there are going to be a lot of answers along the way to the mysteries that people really care about.