Depends. In Plymouth campeigne mission 8 and the starship II colony game: vortexes. you get 2 right next to your base and if you have any building within a certain distance of it, it goes to your base. In the colony game, if you build in the orange area, a vortex comes down and destroys your structure factory at a certain mark. In Plymouth campeigne mission 11: meteors. 60% of the time, you will get an asteroid coming down right above your structur factory. During the missions you have to recover wreakage, electrical storm, as they cause enough damage to slow your units, making them easy targets for computer fire.
Any other time, earthquakes. I've had an entire army whiped out by one, and it was my last defensive line against a computer strike consisting of EMP's and Thor's.