Dr. Nick: So, who killed Kaji? Apparently, just some random Nerv/Seele goon. The "Misato did it" theory was such a stupid early fandom dead end that even the creators themselves took action to kneecap it, as seen in the next cut.
UrsusArctos: No, it was sneaky Sarai all along, damn them! Ancient jokes aside, having Kaji killed by a random goon would make Kaji's death resonate with Misato's death in EoE, also killed by a random goon. Sadamoto's manga, which is his own canon, seems to finger Gendo himself. The events of this episode make Sadamoto's headcanon rather ridiculous, since it's clear that the murderer is acting under orders from Seele to threaten Gendo into obedience.