To capture an enemy base you must first kill off everything within it, then get a unit able to perform the capture into it. Whichever unit you choose for this, will be instantly returned to full health. Any military unit can capture a base except aircraft, transport ships, and probe teams. If the base is a sea base, then you must use a unit able to cross water, be it an attack ship, isle of the deep, or a land unit with the amphibious option built in. You can only use probe teams to do a very costly mind control capture of a base.