Uh, MGS3's ending revolved around the whole deal with The Boss and the set-up with the government and stuff, and the big reveal of whose side she was really on.
Without giving away anything already covered in the other MGS games:
 Spoilers! |
Peace Walker has two endings that are both canon and take place one after the other. The first is about Nuclear Deterrence and The Boss' backstory prior to MGS3. The second, which takes place a little after and is the final ending, is about Militaires Sans Frontiers becoming Outer Heaven, how it started as a group of soldiers who left their countries behind, and what motivated them to become the enemies in the original Metal Gear. It's not "OH WE'RE SUDDENLY EVIL NOW", it just kind of builds, and ends with MSF being a target for every major power in the world, and MSF deciding what it's gonna do from then on. |
Basically, it's not like Star Wars Ep 3 where you see exactly how Anakin turns evil and becomes Darth Vader. You're left with Big Boss somewhere between the tormented guy from MGS3 and the bad guy from Metal Gear, so he's still really likable, but you see the road he's heading down, and that's a bummer.