There's a new Equestria Girls movie coming soon so I shall speculate for the movie.
Even though the film will probably be sports related I'm making up my own plot anyway.
Somehow the balance between the 2 worlds is broken unleashing an ancient evil... It was captive in the gap between the dimensions but when the balance was broken it was set free. It goes around destroying Equestria so the girls use Rainbow power to stop it! However, the monster easily defeats them. So the girls from both universes team up to fight the monster. They have a DBZ style battle and actually come quite close to defeating it when it boosts it's strength and beats them again. So they send a message to everyone in both worlds to lend their energy to them. The girls then unleash the MLP version of a Spirit Bomb and destroy the monster. However, the dark energy from the monster flows into the human world and Equestria where some old foes find it. You hear an evil laugh and the screen fades out. To be contiued in the 2017 movie speculation. Coming soon...