At times, Nabari No Ou literally reads as though the author was deliberately trying to make the characters as gay as possible without turning it a BL manga.
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Where to start...
Technically, it starts off as Foe Yay, but they're terrible at behaving like foes, and after Miharu's Face Heel Turn (or maybe even before, given that he essentially did it so he could help Yoite), it just turns into full-fledged Ho Yay.
Raikou at one point says to Miharu, "You two are a little more than friends." Miharu blushes in response.
In episode 10, too, where they have a moment and Miharu says he's less of The Stoic only when he's thinking of Yoite.
Their reunion in the last chapter.
The panels go from showing them embracing, to just their feet in front of each other. It's like something was suspiciously missing.
The entirety of Yoite's death scene. Most of their flight from Kairoushuu, too.
Yoite's protectiveness of Miharu in general. It definitely transcends the kid just having the Shinrabanshou.
The 2nd ED of the anime features Yoite and Miharu in a Sleep Cute position.
Episode 12 where Miharu worries about Yoite being cold and tries to touch him and Yoite tells him not to worry about him. He also tells Yoite not to die no matter what.
Episode 13 where Miharu worries about Yoite being cold and places a scarf around his neck.
And then there's the scene in episode 14 in the anime where Miharu carries an injured Yoite and Yoite gently caresses Miharu's face with his hand and Miharu gently holds Yoite's hand as he does so. They then hug.
In episode 18 Miharu worries about Yoite again and holds him up when he feels pain. And Raikou says he always pictured that Miharu and Yoite would be together. And Miharu chases after Yoite in the snow when he goes missing. And when he finds him he grabs his hand in his and tenderly hugs him twice which Yoite returns telling him that both of them are "right here".
This scene from episode 22 where Miharu helps carry an injured Yoite and expresses concern for him, telling him that he wants to stay and die together with him. And that they have to leave together.
This scene from episode 26 where Miharu again worries about Yoite and Yoite says he glad he met Miharu, and he leans against Miharu in a Sleep Cute position and Miharu holds him. Also, Miharu holds Yoite's sweater to his face after Yoite disappears and says "I will never forget about you, Yoite."
They're the only characters in the series with matching names who aren't either blood-related or married (Raikou's name literally means "lightning", and Gau's means "rain shower").
Both Raikou and Gau state at some point that they would do anything for each other. Gau is so utterly devoted to Raikou that he's willing to kill himself to make Raikou happier. Raikou, for his part, is protective of Gau to the point that when a mook hurts Gau, Raikou goes completely berserk, kills him, and mutilates his dead body. This theme of the usually unflappable Raikou going crazy with rage whenever Gau is threatened is repeated throughout the series on many occations. Yukimi particularly knows how much Gau means to Raikou and purposefully uses this to escape from him. When Raikou has Yukimi pinned up against a car, Yukimi pulls out a gun and, instead of pointing it at Raikou (who is right in front of him), turns and points it at Gau, who is standing to the side. Raikou allows Yukimi to escape, but then gives chase in anger, promising to kill him.
Hilariously, Gau is actually pretty protective of Raikou, too, and even frets that Raikou will get injured by Yukimi's messy room!
In volume 4, a page from Gau's notebook is visible. Every single entry is about Raikou, ranging from "Raikou-san dyed his hair from green to pink today. I think it suits him" to what sounds suspiciously like the two going on a date, with Raikou taking Gau to Chinatown to buy him dinner.
On the left-hand journal page, which was left untranslated in the English releases, one sentence that features Raikou's name has a few characters scribbled out. Upon closer inspection, the scribbled-out characters seem to be the first two in the Japanese word for "date."
Shijima, calls Gau out on his "affection" for Raikou, making a point about Gau's absolute trust in him. Bearing in mind that Shijima is an expect at observing people and behaviour.
Over the course of the series, they apparently go from living in apartments directly above/beneath each other, to camping together in a single person tent in the middle of the wilderness, to living together at the end of the series.
It's shown in one of the omakes that Gau washes and organizes Raikou's clothes.
The tent that they slept in together has Raikou's last name sewn onto it.
They even get a two-page spread when they're reunited after Gau awakens from his coma, with both of them blushing furiously and Raikou crying with relief. Gau affirming his wish to be forever at Raikou's side.
They touch each other a lot; Raikou stroking Gau's bruised cheek gently with his fingers, resting his hand in Gau's hair to comfort him when he was crying and running his hand over Gau's bandaged chest. While Gau is frequently shown clasping tight hold of Raikou's arms when he's scared and holding Raikou's body flush against his after Raikou is injured but the second Kira user. There is even a color illustration of the Nabari cast, Gau shown clinging to Raikou's arm.
In chapter 48, Raikou finally acknowledged Gau's point of view on Yoite's situation. Until that point Gau had been torn between his debt to Yoite for saving his life and his complete devotion to Raikou. Raikou apologises to Gau, admitting that he "paid no attention to his feelings" and finally completely accepts Gau's wish to stay by his side. He tells Gau not to leave him so he can protect him and that, "I will always be where your hands, your voice or your eyes can find me". Gau stares in surprise, then smiles widely and blushes, running after Raikou.
They also tend to wear matching/opposite color clothing, even when they're hiding out in the forest, completely cut off from the outside world; Gau in white, Raikou in black. Also, in chapter 43 Gau wears the jacket Raikou had been wearing earlier in the chapter, with it draped over his shoulders as the two are walking along in the rain. Implying that Raikou had placed it there, likely to keep him from getting sick in the rain, as Gau had recently been discharged from hospital.
Besides Miharu and Yoite holding hands, this chapter cover features Raikou and Gau staring into each others' eyes while crossing the street.
They also spend their last panel◊ at the end of the series gazing at each other happily. While Raikou is in the middle of talking to Miharu, no less.
They end the series living together happily.
No folder for Yukimi/Yoite?! Those too had at least as many touching scenes together as Yoite and Miharu.