The Master Override was originally created as a means to purge GAIA and her subordinate functions, if necessary. Although Elisabet Sobeck initially resisted Ted Faro's push to install a "kill switch" in GAIA, she eventually relented and installed the master override. 
The override was mentioned by Sylens when he met with Aloy in the GAIA Prime facility. He tells her to purge HADES using the Master Override. Since she has the same identity as Elisabet Sobeck, she is the only one able to enter the room to claim it. Aloy used it to purge HADES and the extinction protocol, thus averting disaster.