Commandant steele opens the vault in time for you to arrive. You arrive and witness a creature emerging and watch it kill Steele. Well, amidst all this havoc, the other atlas guys get eaten, and it's up to you to kill the devourer. It drops to a short endscene, long credits, and a mysterious satellite that says 4N631 (angel in leetspeak) so people can theorize that the satellite is the guardian angel. ANYWAY, you appear back at the vault area where the creature was, you get to pick up it's crap-quality loot, and sell it, then go back and do whatever quests you may have missed, or play through for the second time. - Menkis
[Better summary] After Commandant Steele opens the vault, a massive god-being emerges from the now opened vault, and proceeds to destroy the key-lock, and all of the Crimson Lance troops. The Guardian Angel tells you that the Destroyer is a god in its own realm, but it is vulnerable in this world. The Angel also tells you to attack it in its weak spots, its glowing eye and its mouth. During the fight the Destroyer attacks with mostly tentacle slams, player-seeking spikes and a tentacle spike that comes from its mouth. It has 4 tentacles that extend from its body that count as separate enemies, so destroying one is a way to gain a second wind. After you destroy the Destroyer, the credits roll, and a short video plays showing the original yellow claptrap turning into a Interplanetary Ninja Assasin. After this, the player is allowed to continue the game. The loot found from the Destroyer is usually whites and greens, with much ammo, though any Scavenger COM on Mordecai greatly increases the amount of loot that spawns, and thus the chance of a rare or legendary gun dropping. After leaving the vault, Playthrough 2 becomes unlocked.
Also CL4P-TP (Claptrap) turns into an awsome ninja assassin. - Random Dude Who Actually Beat The Game
you don't actually get to fight it though, it's lame. It WOULD be awesome to fight it though. - Menkis
You do actually get to fight it though, in the latest DLC. - Some other random dude who also beat the game