Three friends work for this organization. They're all Nobodies, people who aren't supposed to have feelings because of some sort of defect of the soul (they don't have hearts), and they're working with the organization to construct Kingdom Hearts, which will either (a) give them hearts, so that they can have feelings, or (b) give them vast cosmic power which they can use for... evil stuff, I guess. You play Roxas. Your best friends are Axel and Xion. Only you and Xion can wield the keyblade, which lets you capture hearts and build Kingdom Hearts... but this is because you contain stolen memories from Sora, the protagonist of the mainline series (the guy spends all of Kingdom Hearts 2 trying to destroy your organization). The organization actually kind of made you both specifically to steal his memories and further their goals. And the only way he can get these missing pieces back, and live again, is if you both give up those memories. Xion figures this out, and tries to escape so she can give back the memories... and Axel keeps beating her up and dragging her back, which makes you feel like crap (yay, you're back... thanks to my violent friend being manipulated by the evil organization... cheer?). She finally succeeds in escaping by getting you to kill her, setting the memories free, which she wanted to do because she's convinced she's not a real person and she's kind of turning into a Sora clone, oh, and also apparently stealing your life essence as well. You go nuts, decide to destroy Kingdom Hearts and find Sora and set everything back the way it was. On your way to do this you get crushed by another main storyline protagonist. End of game.
Dang. Just Dang.