The pyramids were originally built by people, under alien instruction, to act as a charging station for the alien ships. It had something to do with the limestone, gold, and their placement relative to the stars. Some how the alien ships were able to use the cosmic energy, focused by the pyramids, to power their ships.
The only other plausible theory I can think of is that the pyramids were some kind alien "for adults only" toy. Aliens would come here during spring break to use the pyramids.