I just had the idea to make a game in which the whole thing WAS the final boss fight. I'm picturing a space station that the player navigates finding power-ups and chasing his nemesis, and the fighting destroys sections, which the boss then uses to assemble a big robot suit or something. Kind of like Shadow of the Colossus.
Opening scene: The doors to the loading dock are blasted open, our battle-scarred protagonist limps through the smoke and sparks, weapon at the ready. Final boss sits at the controls, lounging as if on a throne and smiling, the helmet to his combat suit under his arm.
Hero: "There's nowhere left to run, Final! All your soldiers are gone, and this time you'll brought down!"
Final: "All this time you think you've been in my way? My dear friend, I wouldn't have made it this far without you! And now we've only reached the beginning!"
Exposition of the story could be built through communication between the two characters, and if the player gets a GAME OVER, maybe they get treated to some flashbacks to flesh out the story more. So instead of death, the protagonist just passes out and loses some of the upgrades the player has collected.
Man, why am I just writing this for a forum thread?