I vaguely remember a Story that essentially built up to the protagonist confronting who we had been led to believe, was the main Villain, only to find out that they've been leading the protagonist around on strings, trying to prevent (or help stop, I forget), some huge calamity.
My Memory is a little Fuzzy, so I do not have any more details, but a good example would be Logan from Fable III or Itachi from Naruto. I know there are a few that would fit this description, but I feel like I would remember it if I saw the name.

Hmm, the only thing I can think of is Ratman... But, the "super villain" is like an anti-hero? Then again I've read this ages ago. My memory is fuzzy. Never did finish it...

Na, Ratman's diffrent than what I am looking for. I know its kind of hard to pin this one down, but like I said, if I see the title, I feel like I'll remember it.

Anyone have any idea? this is driving me mad.

I know many series like that but your statements are too general since all you said was main villain training main character in secret.

I think the one you're thinking about is Hitman Reborn where they raided a facility to take out the boss but it turns out it was all a hardcore training exercise.

I got nothing besides the above as a hunch, however you should check this out if you want more chances of recalling it.

http://tvtropes.org/pmwiki/pmwiki.php/Main/StealthMentor

Yes and no? The "Stealth Mentor" concept is similar, but more mixed with "Necessary Evil" trope (I'd give it about 30%/70% split).

Like I said, Logan (fable 3) is a good example; He was most definitely the "Bad Guy", but everything he did, he saw as nessisary to beat The Darkness.
Itachi is another good example; you can not call him a good guy, but his whole goal was to make Sasuke Stronger.

Anyone have any other ideas?