The Command Center is a large administrative building serving as regional headquarters for GDI forces. They are typically built in large GDI bases or depots.
In Reaper Raid, a GDI Command Center is located to the left of the Goliath Tank supply depot. When attacked civilian scientists will start exiting and panicking. A health crate will appear if the building the destroyed.
In Eagles Fall, Owen's Command Center is located in the center of the GDI base complex. It is the primary target to be destroyed in the mission.