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: That would make Kaji's death resonate with Misato's death in EoE, killed by a random goon. Sadamoto's manga, which is a different continuity, strongly implied that Gendo himself was the murderer. That's purely Sadamoto's headcanon since there's zero evidence for that in the anime.