The old man (John Doe) beaten up at the beginning of the film turns out to be God on her (Alanis Morissettes) yearly visit to earth. She just loves playing Skee-ball.
Matt Damon and Ben Affleck are fallen angels who have found a loophole to get back into heaven.
In order to do this, they must become human. When Matt Damon becomes human, he gets a sudden burst of conscience and decides not to go back realizing that it would unmake the world if they proved God wrong. A furious Ben Affleck stabs and kills him.
No human hearing God speak can withstand the mightiness of God, and will die. When God speaks (if you can call it speaking) to the now human Ben, his head blows up ( in the tradition of Scanners).
Linda Fiorentino is the last scion.The last living relative of Christ.
She realizes the John Doe beaten up in the beginning is actually God. So to prevent Damon and Affleck from completing their goal, she pulls the plug on the old man, bringing her (Alanis Morissette) back to life as God. In the process she dies because she couldnt handle the power that is God.
After Ben Afflecks death, God brings Linda back to life and impregnates her with the next scion.
When asking God "Why are we here?", God touches Lindas nose and says... boop