The Original Neon Genesis Evangelion ends with a lot of unanswered questions. Sometimes, it's because the end of the series was rushed due to behind-the-scenes production problems. Other times, things were deliberately left open to interpretation for the fans. Then there are the simple oversights that lead to plot holes. One of the questions raised by this ambiguity regards the assassination of Ryoji Kaji.
Kaji's death is mysterious because nobody knows just who killed him. It's heavily implied he was shot to death, but the audience is never shown so much as a handgun sticking out of the edge of the screen. There have been several theories put forth, but nothing concrete has been established. Here's everything that's known about Kaji's death and what conclusions have been drawn.
Understanding who would want to kill Kaji will require some context regarding who the man was. Initially, he was introduced as a special inspector for NERV. The truth, however, was that he was a spy for SEELE. Whatever the situation, he was always cool, calm, and collected, rarely showing any signs of vulnerability; an Angel could be attacking nearby and he'd just be casually watering his plants. He was also a notorious womanizer who liked to flirt with the NERV female staff, especially his ex-girlfriend Misato Katsuragi.
The murder took place in Episode 21 of the anime, "The Birth of NERV." The episode featured Kaji betraying SEELE by rescuing Kōzō Fuyutsuki from their custody. This was despite the fact that he was the one SEELE originally ordered to kidnap the NERV Deputy Commander. Later, while he was by himself, he casually looked up at someone and said "You're a little late, aren't you?" before the screen faded to black and a gunshot was heard. He was clearly expecting and ready to die.
Many believe that whoever did Kaji in was a member of either NERV or SEELE. By this point, it was obvious that he was working on both sides and doing whatever he liked. Kidnapping and then rescuing Fuyutsuki could have easily incurred the wrath of the higher-ups from either organization.
One of the people fans have theorized is the killer is Misato. A lot of this has to do with what happens in the episode. When Fuyutsuki is first kidnapped, Misato is approached by men from NERV Intelligence due to her relationship with Kaji. Later, when "a solution has been found," she's given her gun; she asks where he is, though the person he asks doesn't know. Between this scene and her next scene, Kaji is killed. The episode ends with her coming home uncharacteristically depressed; she Kaji's last message to her over the phone and breaks down crying. Everything about how her story is presented makes it seem like she's directly involved in the murder.
This theory has been debunked by NGE creator Hideaki Anno. He expressed shock about this conclusion and addressed it in an interview for Newtype. He suggested that the act was instead carried out by the Japanese Government or a SEELE agent.
The blame on Misato is further deflected by NGE assistant director Kazuya Tsurumaki. In an interview with FUNime, he elaborated that Kaji, while looking deeper into NERV (SEELE), was tricked by one of his informants and killed. He also said that Ritsuko wasn't responsible, either.
The "Director's Cut" version of Episode 21 adds a scene to suggest it was SEELE that did Kaji in. It's "revealed" that Kaji delivered a sample of Adam to Gendō. This, along with freeing Fuyutsuki, adds to the precariousness of his connection with SEELE, which further suggests that they were the ones who wanted him dead. This is seen as one of the anime's only major retcons.
The manga done by Character Designer Yoshiyuki Sadamoto has further implications about the killer. When Kaji is assassinated, he's shot twice and remarks that the killer is a poor shot. This could imply that the killer was somebody in power rather than a trained assassin. The manga isn't necessarily canon to the anime, but given who wrote it, it's worth keeping in mind.
Another possible killer is provided by the game Secret of Evangelion. In this game, the protagonist is Kyoya Kenzaki, Kaji's old friend who is looking into the secrets of the Human Instrumentality Project and Evangelion Unit-04. One of the events of the game has him kill Kaji. Again, this isn't canon to the anime, but it's the only instance in the franchise where Kaji's killer has a face.
Whoever killed Kaji remains largely a mystery. In all likelihood, it was always meant to be some hired gun of SEELE's whom nobody was really supposed to care about. None of the NGE staff could have predicted how much this vague death scene would gnaw at the back of the fans' minds.
