If you haven't beaten The End within two weeks of starting the battle, the next time you load your savegame a cutscene shows he has died of old age. He is replaced with a ninja squad you have to evade/defeat in the jungle.

You can also kill The End using a sniper rifle the first time you see him in the game (right after emerging from The Sorrow's boss "fight"). You have to snipe him while he's sitting in the wheelchair before he's taken away.