Ryoji Kaji is probably the coolest character in Neon Genesis Evangelion. He was a "Triple Agent", working for the Special Inspections Division of NERV, the Investigations Department of the Japanese Ministry of Internal Affairs, and also directly for SEELE. He was the "James Bond" of Evangelion, he did all the cool stuff, he slept with the hottest babe (Misato Katsuragi), he was always searching for the truth, and in the end his actions brought about his demise. In Evangelion Episode 21, with the famous last words " Oh, what took you so long?", the gunshot sounded and Kaji was killed.
Debate has raged for years among Eva no Otaku over who shot Kaji. We never see the shooter, never hear them speak, we only ever see Kaji greeting them (nonchalant as ever) and then hearing the gunshot.
First I shall attempt to squash any ideas that Kaji wasn't even shot, that it was all
an elaborate ruse. This theory circulates most among the legions of devoted Kaji lovers
out there, who can't stand to believe that their favourite character was shot and killed.
Discounting all the evidence in the series that suggests Kaji was shot, (Misato crying
over the answering machine, Asuka suggesting in Episode 22 when the phone rings and it
could be Kaji, and Misato saying that it can't be him, in Redone Evangelion Episode 24
Shinji comes straight out and tells Asuka that Kaji is never coming back, but Asuka says
he is lying), it states directly in The End of Evangelion - Theatrical Program, which is
an official canon document, that Kaji was shot to death. He is dead.
But who killed him? Who shot Ryoji Kaji?
A lot of Japanese viewers thought that Misato Katsuragi shot Kaji. They believed that because you see the door of Misato's apartment closing just after the gunshot (you see the name plate on it saying "M. KATSURAGI"), it must mean that Anno Hideaki (the director/creator of Evangelion) wanted to hint that Misato killed Kaji. Anno never intended this cut to be a clue of any sort. In fact he was taken aback when he heard that's fans thought it was Misato. He stated directly that it wasn't Misato and he even edited Evangelion Episode 21 for the Japanese Video release to remove the cut of the door saying "M. KATSURAGI") and just putting in a cut of the street instead. He removed it because he didn't want people thinking it was Misato! He was actually shocked that people thought it was Misato and was embarrassed that people thought they found "hints" where there were actually no "hints" at all. Some also point to where Misato threatened to kill Kaji in Evangelion Episode 15 as proof that she actually did in Episode 21. This doesn't hold up though because by Episode 21 (and this is show specifically at the end of Episode 20) Misato and Kaji are both doing the same thing, "looking for the truth", after Kaji is killed the baton is passed onto Misato to uncover the "truth".
Anno has said straight out that it wasn't Misato who shot Kaji. Also in the "Checkpoint" section of the official film book, it states that the person who shot Kaji was not a main character. It was some nameless security officer from either NERV or SEELE.
In the original scenario for Episode 21 there is a scene where one of the NERV security officers enters Gendou's office and tells him that Fuyutsuki has returned but that they couldn't find the man who kidnapped him (which of course is Kaji). Then the scene that follows is where the NERV security officer goes to Misato, gives her gun back, and tells her that "it's over now" and that they "don't know where 'he' is". It seems clear that nobody at NERV knows where Kaji is.
SEELE would though. In Evangelion Episode 20 SEELE refer to Kaji as a bell attached to Gendou Ikari's neck but which doesn't ring. Then they say that they will make the bell work. Kaji kidnaps Fuyutsuki for SEELE, but then in the end he frees him. In the redone Evangelion Episode 21 there is added dialogue between Kaji and Fuyutsuki, Kaji is warned by Fuyutsuki, that by freeing him is probably going to get him killed, by Kaji replies that "They", referring to SEELE, have found out that Kaji stole Adam (in Evangelion Episode 08) from them and gave it to Gendou. The passage is as follows:
Fuyutsuki: It's you.
Kaji: It's long since the last time.
Fuyutsuki: This action will result in your death.
Kaji: I just want to get closer to the truth... the truth within me. Besides, it seems they're catching on to the fact that I smuggled the Adam sample for Commander Ikari. If I don't start looking out for myself, things could be looking grim... for me.
It seems clear that SEELE wanted Kaji killed. As to who shot him, well Anno has said it wasn't a main character, that it was just a security officer. There is not "hidden truth" to Kaji's death, SEELE had him killed, not in an important way, they just sent a security agent to shoot him. Kaji faced death, as he had always faced life, with the indifferent coolness that won him so many fans. Ryoji Kaji rest in peace.