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A lot of people assume it was Misato, because 1) Kaji greets the shooter as if it were a close friend. and 2) Misato shows a reaction to the message on the machine before she even listens to it, and seems to immediately know it's him. But both these points kinda suck. 1) Kaji is just Kaji. He greets everybody as if they were a close friend, and he was totally expecting (if not waiting, as he is shown) to be assassinated. 2) After the hours of tension in the jail and then suddenly being released, going home and finding a single message on the answering machine, Misato could only assume one thing had happened; and that was that Kaji was taken down by someone, but someone other than her.

I'm going to assume it's a Seele agent. Kaji quadruple crossed Seele by letting Fuyutsuki go, and even Fuyutsuki said "You'll probably be killed for this, you know that right?" Not to mention Kaji had been stepping on everybody's toes by double crossing and digging deeper for the truth.

Should wouldn't kill him because she was horrified of loving him. In fact, even after she killed him, she was dedicated to completing his investigation into Nerv and Seele's secrets and openly speaks about doing it for "her love" Ryoji Kaji.

And Kaji is always calm. He's calm and sly when talking to anybody. He flirts with just about everybody and always seems cool and on top of things, even when an Angel is attacking. In episode 19, he's standing there, watering his melons while Zeruel is blowing s**t up, and he just stands the coolly, giving advice to Shinji. The way he acted right before he got shot was classic Kaji attitude right there, and in no way influenced by Misato.