You do realize that Condition Green requires shields to be lowered and weapons to be powered down? If you try to re-raise the shields, you will immediately go back to at least Yellow Alert. If I remember the settings correctly, the only combat system that still functions (and by function I mean cycle) is ADDs, Plasma Ds, and Drone Racks. Phasers can be charged at Yellow Alert. Note that none of these systems will actually discharge at condition green or yellow, they will simply cycle/charge. You need active fire control, which is only at Condition Red, in order to actually discharge those weapons. Any time a heavy weapon hard point is brought online, your ship is automatically set to Condition Red.