Prior to Gorod Krovi, the last we had time we heard mention of Sophia was in Der Reise. Then we were introduced, rather suddenly, to S.O.P.H.I.A, the Strategic Operations Planning Heuristics Intelligence Analyser.
This robotic version of Doctor Maxis' secretary is odd, expecially when you consider Richtofen's quote upon meeting her in Gorod Krovi.
"Uh... Believe it or not, S.O.P.H.I.A used to be Maxis' secretary. How she became a machine, I know not."
This is proof that Sophia was not always an Artificial Intelligence, and the histroy to her transformation has been revealed in a radio, found in Revelations.
"After weeks of failure and concentration, Dr.Maxis finally achieved the breakthrough he had been searching for. The results were immediate and startling. In the case of subject 26 his instances of violent outbursts were non-existent. His docility appeared permanently. Unfortunately while we prepared to implement the treatment on the other subjects, there was… an incident. During his field tests this morning, Subject 26 attacked a handler. 26 and the handler were both destroyed. Maxis believed that 26 only attacked the handler. He does not know I was attacked as well. I have observed a developing pattern of high fevers and cold sweats. My thoughts are erratic. My relationship with Ludvig is complicated. I fear I cannot keep this secret from him for long."
It's clear that Sophia met a similar fate to Maxis in Origins. Slowly succumbing to the bite she recieved, her brain was removed and her consciousness was placed into the machine we see in Gorod Krovi, saving her from turning. It isn't clear who went through the process of removing her brain, but it is clearly not Richtofen, at least not this Richtofen.