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A system interlock was a function of the transporter used to synchronize the pattern buffers of one or more transporter devices. The system interlock was essential to proper and safe transit between two connected transporter systems.
Engaging the interlock could cause ionic fluctuations to occur within the matter stream during transport. This was the case in 2369 when Reginald Barclay beamed back to the USS Enterprise-D from the USS Yosemite in the midst of a plasma streamer. Because of this, Barclay was able to see the quasi-energy microbes (actually members of Yosemite's crew) that were trapped within the matter stream. (TNG: "Realm of Fear")