These Replica soldiers only appear while moving through the Armacham Technology Corporation access tunnel underneath Fairport, in the tram area before reaching the cooling systems of the Still Island nuclear power plant. It is possible that these Replicas were deployed in an emergency to stop Dark Signal from reaching Still Island and were simply not fully equipped when encountered. This is supported by the fact that Michael Becket only encounters them while moving through an ATC storage facility, and the deformed Replicas only appear after emerging from their stasis pods.