When English-speaking fans begin to talk about a Japanese anime, there's usually a problem with spelling Japanese names using the English alphabet. Other sources will spell names differently. No attempt at keeping the spelling scheme consistent was made for this page. Rather, the more common spellings were used.
Anno himself, yes, the Anno, has said (as quoted in published sources), that the killer was some third party, an agent working either for SEELE or for NERV's Intelligence Division. Kaji simply found out more than he should have and he needed to be silenced.
The theory that Misato killed Kaji continues to circulate, perhaps due to the continued existence of websites that blame Misato. However, Anno's comment seem to indicate that Misato did not do it. She is definitely not a "third party" in the story. She is one of the main characters. Furthermore, even the newest newbie can testify that she is "Misato, Director of Operations," not "Agent Misato, Intelligence Division."
Finally, everyone's deepest darkest secrets were brought to light in Human Complementation. If Misato killed Kaji, how come this was never discovered in Human Complementation?
Most likely, no. Naoko was very much alive and still had her brain intact and in her possession when the Magi were finished, completed, and in no way did the Magi need her brain. After the Magi were completed, she continued to work for GEHIRN up to the incident when she throttled Rei, meaning she still had her brain with her. She killed herself by jumping off Central Dogma and probably suffered massive head and brain injuries in the process after Magi were finished, completed, and in no way did the Magi need her scattered-into-pieces brain.
Naoko imbued the Magi with her personality traits, however. Caspar was programmed to behave as if it was Naoko's "mother" aspect. This is why Ritsuko referred to Caspar as "mother." This is poetic and deeply symbolic and full of irony, since Ritsuko never thought that Naoko was a good mother (but Ritsuko had to maintain an intimate working knowledge of the Magi since that was part of Ritsuko's job). This is drama, and this should not be taken literally to mean that Naoko's brain is in Caspar.
Finally, the "brain" that we see in Episode 13 is not Naoko's. In fact, it is quiet likely that it's not a human brain at all. No blood and life-support fluids oozed out, and it has these nice little holes for wires to go into. Most likely, it is an artificial "brain" that provides the artificial intelligence for the Magus Supercomputer. It could be made out of synthetic material, or it may actually be living tissue that was artificially grown for the purpose.
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