1999 chevrolet malibu overheated and now it won't start. What could be the issue?

I'd have to be sure engine isn't seized, turn the crank by hand. You could remove belt and spark plugs then try to turn crank by hand. If hydrostatic lock, the fluid should come out of spark plug hole. With it overheating, you may have internal engine damage? Are you saying it cranks good but won't start or the starter motor won't crank?

Just to add, make sure battery has a full charge.

The car acts like it wants to start. The lights come on, its just won't turn over.

First I would try squirting some oil in the cylinders to raise the compression. If it fires off just run it a bit, then do a compression test. That is an aluminum head on there and it don't take much to warp it, causing bad head gaskets. A compression test would show 1 or 2 low cylinders if the head gasket is bad.