I've watched the Animatrix and all the fan material on this theme over the years. There is a cute short backstory to cipher that I cannot remember exactly, nor where to find it. It basically elaborated on the part where "Morpheus" says they have a rule about awakening old minds. That usually the subject cannot take it and breaks. It may not be about cipher exactly but it's along the same lines. He snaps in Zion and murders a whole bunch of people because his mind couldn't adjust to reality. It's powerful stuff and more relevant today than most people would recognize.