So what was the plan for a sequel?

marky would be stuck in an ape alternate timeline version of our own planet, he gets busted out of prison by some underground ape organization that helps him find an ape scientist who can help him get back and fix his space ship and then get back to that space time warp thing, while also falling in love and fighting in an ape revolution against the ape government and then having to choose between love and leaving.

If you listen to Tim Burton's commentary on the DVD, they didn't have a plan at the time. The ending was forced on him by the studio to set up a sequel. Since the movie bombed, a sequel was never written.