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 after GAIA herself agreed. 
The override was mentioned by Sylens when he met with Aloy in the GAIA Prime facility. He instructed her to purge HADES using the Master Override. Since Aloy was genetically identical to Elisabet Sobeck, she was the only one able to enter the room to claim it. Afterwards, Aloy installed the Master Override inside Sylens' Lance, carrying it with her from then on. Aloy eventually used the override to purge HADES and the extinction protocol, thus averting disaster.