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Since 2521, the military operating systems had been standardized for over 70 years, leaving them vulnerable to hacking. There were several incidents, the most prominent being with the destroyer UNSC Persephone, in which the systems were hacked. This prompted Dr. Halsey to create new protocols.
The algorithms were based on already existing translation algorithms.
The so-called 'c-pies' were mainly created by Dr. Halsey for use in the third-generation Smart AI's. This new crop of intellect would allow them to penetrate any system software. A side effect of the protocol was that the A.I.'s could learn to mutate and defend established UNSC operation systems from attacks.