Bioshock Infinite, at the end I didn't know what tha fudge happened. Had to watch a video on youtube to barerly understand the paralel timelines and the chronological order of the events.

What's wrong with the MW campaigns? The plot seemed pretty straight forward.

As for the invasion mission ("Wolverines?") they explain that clearly. Russians recovered that ACS thing from the second mission and that allowed Russia to launch a sneak attack. It wouldn't happen in real life, but that's fiction for you. 

Donkey Kong :P

Of course not, but they're asking for silly stories and that one came to mind. I usually love somewhat wild stories but generally prefer that they make sense within the context of the game's world.

I'd go with Bioshock: Infinite. I was completely lost by the end of the game. Even after reading some wikis online, I still don't feel like I truly understand everything.

Having not played Kingdom's Hearts, I'll go with Metal Gear for now, though Five Nights at Freddy's is quickly approaching it.

I actually thought the campaigns were fun and I'm specifically referring to the last missions of the second. Obviously the first thing I thought of was Red Dawn haha, but even with the fact that it was a sneak attack (let's ignore just how they actually made the long flight over the arctic) it was just so over the top. They dropped thousands of men and, do recall, a ton of armored support into a city of large symbolic import but, given the surrounding bases (including battle-ready tanks), is essentially suicide to parachute into. They lack the capacity to pull off a covert air drop like that given how much friendly territory they'd have flown over, would never want to in the first place, and would be immediately overwhelmed and completely without any logistical support whatsoever. It would make Market Garden look like a resounding success.

I know I'm being a party pooper that's overthinking the game (I can see it as I read my own words haha), and generally I'll go along with any crazy story as they're usually far more fun. I guess why this one bugged me was, for nearly two complete campaigns, the world was very much tied to our own and, while we ourselves were over-the-top supermen, it all felt somewhat realistic as we fought the still-realistic-threat that a terrorist organization might acquire nuclear weapons. I guess I liked it for that reason, and so was rather disappointed when I was suddenly not only fighting Russians in the US simply because of a dubious possibility that the U.S. was solely behind a terrorist attack in Russia, but we were actually losing despite having every possible home field advantage. Heck, in the game they represent the EMP as having given the U.S. a chance to retaliate, when in reality that'd be a godsend to Russian forces surrounded in enemy territory. None of it really made any sense to me.

I don't want to keep complaining as it suggests I didn't enjoy the game (I did). I suppose it just seemed out of place with the first 1 1/2 campaigns, and I'm admittedly more of a stickler when it's suggested the game takes place in our real world. Maybe I've played too much Hearts of Iron.

I dont see convoluted as a bad thing. I actually enjoy complex plots.

What i dont enjoy are dyslexic, nonsensical plots, like FFXIII.

Of the games I've played, Kingdom Hearts takes the cake.
I think my brain just turned off during the cut scenes after a while.

I cant pick any off the top of my head, but generally Japanese games have convoluted plots, especially JRPGs.