Right, so I want to let you know how you could have worked out who the killer was. It’s not easy, but there are a few ways you could have done it by using logic and asking the right questions.
1) Let’s start with the hospital room. We know that Matsuoka’s eyes have been transplanted into Himura’s face, and we know about a mysterious operating room in an abandoned hospital that’s been cleaned recently. There are two paths from this.
Firstly, if Kawaguchi was the killer, why would he invite Tenzou to the ghost town and let him search in the direction of the hospital where he might stumble across the operating theatre? He could easily have avoided Tenzou discovering it by pretending to check the hospital himself and saying he’d found nothing.
Secondly, Tenzou noticed that the debris from the room had been cleaned into the prep room and there was no blood. This implies that the room was cleaned before whatever happened there (as well as after, when the evidence would have been disposed of more thoroughly). The hospital is filthy and unhygienic but functional – we can deduce that Matsuoka’s eyes were removed here (we know they were taken illegally because why else would the body have been hidden?) and that’s why the room was cleaned beforehand.
From this, we wonder: were Matsuoka’s eyes taken to the hospital to be transplanted? But this is problematic, as Kakashi notes, because hospitals include a lot of paperwork, and there would have been multiple people involved in Himura’s surgery. Someone at some point would have wondered about the donor. It’s not normal for surgeons to bring their own body parts for transplants. So Himura must have also been present at the old hospital and the transplant performed there. Since Kawaguchi isn’t a genjutsu user, there was no way for him to convince Himura he’d had the transplant in the new hospital, so Himura must have knowingly gone to the old hospital and received the transplant there.
Kawaguchi has been discounted and Himura must have willingly accepted illegally harvested eyes. Therefore Himura must be 3am.
2) Right, this one is much harder to get, but I’ll go through it anyway. 3am is very, very smart. We know this, we’ve been shown it and told it multiple times. Naturally, he’d have someone in mind to frame for the murders. There are two possible frame jobs presented in the story.
First, Kawaguchi steals the mask and uniform. This is such an obvious frame job that we start to doubt it. Surely 3am is too clever and could come up with something subtler. Maybe Kawaguchi is using a double bluff. It’s risky but possible.
Second, the calling seal is found in Haruki’s room. Kawaguchi finds this when he’s alone and could well have planted it. However, it’s also possible that Himura used genjutsu to make Haruki plant it himself.
The question is: if Kawaguchi is smart enough to fake his own frame job, why would he choose Haruki to frame? They have a difficult and antagonistic relationship and it seems clear that Kawaguchi would be motivated by revenge. But it’s not a secret that he dislikes Haruki – he proclaims it to anyone who asks. So isn’t it too obvious? Whereas Himura wants someone to realise it’s a frame job so being too subtle wouldn’t work in his favour.
The real flaw in Kawaguchi framing Haruki, however, has to do with the timing. Iruka has survived the attempt on his life and we suspect he was targeted because of knowledge he has about the scroll that was probably used to create Himura’s seals. Whatever he knows is dangerous and could possibly unravel the whole mystery. Therefore, it’s likely that 3am will make another attempt on Iruka’s life. At the point where the calling seal is found in Haruki’s room, Iruka is still safe and alive, but if Haruki is arrested before Iruka’s death, who could Kawaguchi blame when he murdered Iruka? His other suspect/scapegoat is Kakashi, who is the obvious answer to Haruki’s alibi for the night of Kaede’s death, but if Kakashi’s motive for killing Kaede is revenge for Iruka, it becomes impossible to also frame him for Iruka’s death. Therefore, the whole Haruki/Kakashi narrative is thrown into doubt. Whereas Himura can only plant the calling seal – he can’t control or predict when it’ll be found, so he’s more likely to make a mistake with the timing.
Therefore, either Kawaguchi is making a huge miscalculation and not planning ahead far enough (which is highly uncharacteristic of 3am), or he’s discounted as a suspect. This leaves us with Himura by process of elimination (because Haruki’s in jail when Iruka is kidnapped, so he’s not a viable option).
If you’re really astute, you can actually take it a step further. Let’s consider what it means to frame someone. The killer shifts blame to someone else by making people believe that the framed person is acting like the killer. Circle that around a few times. What is the killer doing? Framing someone. So how can he make it look like someone else is the killer? By making it look like they’re framing someone. Actually a very simple idea but it does take some lateral thinking. Hard to get, but we’ve already been introduced to the concept of a double bluff with Kawaguchi ‘framing’ himself.
(That one was super tricky, I didn’t expect anyone to get through all the layers, but even if you just found it problematic that someone as smart as 3am/Kawaguchi was framing someone as obvious as Haruki then you were on the right track. The timing was the key clue though).
3) Profiling the killer. 3am kills his victims in a very cruel way. He renders them helpless by tying them down and using seals to prevent them from attracting help. He chooses to kill them while they’re sleeping in their own beds, the place where they should feel safest and most comfortable yet where they’re also at their most vulnerable. The attacks use great strength and violence and the killer watches his victims until they give up struggling before leaving them to die slowly.
What does this tell us about the killer? That to him, these murders are personal. There’s anger and a desire for control, to make the victim lose hope and be aware of their impending death. There’s also something ritualistic about the deaths, and it goes against normal shinobi practices of making sure of a kill and killing an enemy as quickly as possible. The act of killing isn’t just functional, it’s sating some obsessive need for control that overrides everything else. Yet there’s a contradiction – 3am wants to watch his victims suffer but not watch them die. Whatever he’s looking for in this ritual is satisfied by the suffering alone. The deaths themselves might even distress him, prompting him to leave so he doesn’t have to see them.
The killer also wears ANBU armour – this is a brilliant disguise since ANBU can move freely, but why not use a henge? Stealing the armour was a needless risk. Clearly 3am’s ANBU identity is very important to him and is a key part of his motivation.
So let’s compare this profile against our two suspects.
-Has a difficult history with active shinobi duty. Spent his whole childhood avoiding being sent into combat and was extremely reluctant to become an undercover agent. So reluctant that he’s held a grudge against Haruki for over a decade. His attitude towards ANBU may be different, but to such an obsessive level? It’s unlikely.
-If he’s 3am it’s to help Himura regain his sight. He has no personal connection with any of the victims (except Akane) and his emotional investment would be secondary, on Himura’s behalf. So why would he need to kill the victims in such a needlessly cruel way?
-Comes from an espionage background where discretion and subtlety are key. Doesn’t fit with the ritualistic murders or the clear emotions on display.
-Stopped being not only ANBU but an active shinobi when he lost his vision, and became depressed over it.
-If we theorise that he’s 3am, the reason for the murders is clearly to cover up his eye transplant. He feels strongly enough about regaining his sight and active status to undergo an illegal surgery and murder others who might discover it.
-Immediately applies for active status and ANBU membership after regaining his vision, despite the fact that he’s just lost his girlfriend. Very keen to get back to work, not taking the time to grieve.
-Felt useless and helpless while blind. The same emotions he incites in his victims. An attempt at catharsis, perhaps, or a way to regain control and re-validate his strength and ability.
By profiling, Himura is a much clearer fit. The main problem with his profile is Akane’s death and Himura’s clear love for her. However, if he was willing to sacrifice his morality for his eyes, can we be sure he would draw the line at murdering his own lover? Especially if he suspected that she didn’t love him enough to prioritise his sight over the lives of strangers whereas Kaede, a total stranger, was willing to make that sacrifice.
4) Let’s look at the physical evidence for Kawaguchi and Himura.
-Checked the scroll out of the archives in the right time period
-Was caught on camera stealing the mask and uniform
-Tangible connection to Akane and Himura (and technically to Eri, who would have given him his ANBU tattoo)
-The seals on his face
-Someone else’s eyes in his face
-A tangible connection to all of the victims except Matsuoka and Iruka (who are both, however, strongly connected to Kaede. Matsuoka is connected to Himura’s eyes and Iruka is connected to the seals)
-A tangible connection to Kaede
-A tangible connection to Kawaguchi
There’s also the calling seal found in Haruki’s room, but we can’t physically link it to either Kawaguchi or Himura, and both of them have had the opportunity to plant it.
It’s much easier to find reasonable explanations for the evidence related to Kawaguchi than it is for Himura. We already know that Kawaguchi might have been under a genjutsu and while it looks like he might have been involved with the seals research, that’s not inherently damning. After all, Akane was involved with the research and she was a victim rather than the perpetrator. In fact, a connection to the research is statistically more likely to make the person a victim, and if Kawaguchi was under a genjutsu, he’s a victim too. You obviously can’t prove anything through solid evidence (or Tenzou would have figured it out long ago), but it does place Himura right at the centre of everything.
There’s also a lot of circumstantial evidence, but I’m not going into that simply because there’s way too much of it. And when solving a crime, physical evidence is much more important, so you should have been giving it higher priority.
There are potentially other ways you could have worked it out, but those are the main ones. I know none of them are easy, and they all require a level of extrapolation, logic and deductive reasoning, but it wouldn't be half as fun any other way ;)