I found the alternate ending to the game! You get it by choosing to save Ann instead of the world--Ann is on the right side of the screen hanging off a ledge when Rufus is throwing rocks and energy at you, and if you make it to her position, Jekyll will automatically take control from Hyde and pull her up.
This leads into a scene where Rufus and his father succeed in calling down Kronos, plunging the world into ruin, and Jekyll and Ann embrace as the world falls apart around them.
Here's a picture as proof!
So the ending most people get, where
the world is saved but Ann dies
seems to be the better option. XD