One True Three

Q: Is Kanji with Rise, or is he with Naoto?
Reviewer Kisdota, The Freak Gamer asks: Are you giving hints at Naoto/Kanji?

A: Both.
The answer to this question is actually explained in Chapter 14: Past Transgressions. In that chapter, Rise reveals (among other things) that she is at the very least having sex with Kanji. Chie and Yukiko are somewhat surprised to learn this, as they have for a while thought that Naoto and Kanji were a couple (I have taken this couple as canon, based on some of the events in the game, and the relationships expanded upon in the drama CD). Rise then explains that Naoto is with Kanji, but that she has to share him because "he's just so big."

This conversation was written mostly for humorous effect, because Rise is so straightforward with everything and anything that has to do with her own (or anyone else's) sex life. But it also sets up the idea that Rise, Naoto, and Kanji are in a "non-traditional" relationship, between the three of them.

Later in the chapter, Naoto explains the feelings between the three of them in somewhat less graphic detail:

Naoto hummed. She inhaled deeply, almost like a sigh. “There is a deep bond between me and Kanji-chan. We are drawn to each other for very specific reasons.” She chuckled again. “But he is drawn to Rise-chan, as well, for other reasons that I can understand. I am drawn to her for those reasons, too.”

Chie sniffed and looked at the younger woman in some surprise. “You mean, the three of you...together?”

Naoto smiled back at her, softly and with a subtle blush along her cheeks. “Neither Kanji-chan nor I discriminate on the basis of gender. So, we share.” She reached out and touched Chie on the hand, her expression turning serious. “As much as we may tease her, and as much as she may still act a flirt, Rise-chan is not the same frivolous woman she once was. I have been close enough with her these last two years to have felt the full power of her love, and to know unconditionally that the whole of her heart is devoted to me and Kanji-chan.”

When I played the game the first time, I thought that Kanji and Naoto should have ended up together. But then I started seeing glimmerings of Kanji/Rise, and I thought that they made a cute couple, too. And then I started to see Naoto/Rise start to pop up, and I thought, Why can't the three kouhai form a threesome? The three of them have complementary personalities (Kanji is the gruff sweetheart; Naoto is the cool professional; Rise is the bubbly perpetual girl), and they're also physically attractive as a trio. So, I made them my "One True Three," as opposed to a "One True Pair" (OT3 and OTP, respectively).

Maybe Kisdota, The Freak Gamer forgot about what was said in Chapter 14 (it has been a long time since that chapter was posted), or maybe he came in after the fact. But, yes, there are very strong hints of Kanji/Naoto. There are also very strong hints of Kanji/Rise. And there are less strong hints about Naoto/Rise...although those will become less subtle as the story progresses into the final arc.