Before he comes into the scene from below, you see his metal box broken open and a technician down on the floor. Why he would have been taken to Cybertech's facility, definitely is a plot-hole ignored for the very fun pay off of killing him off comically and without question.
Very Wheddon-esque thing to do.
They didn't take Garrett there, that was where they took him into custody... It appeared to me that he had overpowered his guards before they got him out of the building and had gone to the Deathlok regeneration room to get an "upgrade" before fighting his way out of the facility.