The way out is through a hole in the floor in the area to the right of where you will have killed the controller mutant after turning off the last switch. This hole leads you into the sewers and eventually back out near the swamp - watch out while you are in the sewer as there are a few things waiting for you.
Near the controller mutant, but on the left hand side, loot Ghost's body which is in the same area.
Hope this helps
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