The Ghost Academy makes the Ghost available for production as well as making certain upgrades researchable for it. It also builds Nuclear Missiles, which the Ghost can launch with the Tac Nuke Strike ability. When launched, the Nuke exits out the top of the Ghost Academy. A Ghost Academy can only have one Nuke armed at a time.
The Ghost Academy used to be called Shadow Ops. This name passed to a different building whose name is now the Merc Compound.