While their relationship during their school years is a bit unclear, in Danganronpa IF it's stated that Makoto had a crush on Kyouko and Junko described her as Mukuro's "rival in love" due to Mukuro's secret crush on him. However, it's not mentioned how she felt about him. Since Makoto is originally shown interested in Sayaka, this seems to imply that at some point his affections turned towards Kyouko (regardless, he and Sayaka are shown to be close friends in Danganronpa 3). In a high school picture, Makoto seems to be looking at Kyouko and Sayaka while their class was out swimming.
During the Killing Game, ever since the first murder, Kyouko became closer to Makoto, evident from her later interactions with him, hinting some sort of mutual attraction. Kyouko also helps Makoto solve each Class Trial whenever he is out of clues. Both are on good terms with each other, Kyouko trusts Makoto (although just for her plans against Monokuma) but Makoto puts his trust in her completely as he hopes that she would trust him as much as he trusts her. Regardless, Kyouko seems to care more for Makoto as time goes on. Evidence was shown when she entered his room and told Makoto to beware of Mukuro. She also saved him from Junko (thought to be Mukuro) who was about to kill him when he was asleep. When Makoto allows himself to be found guilty in Chapter 5 (though he's saved at the last minute by Alter Ego), Kyouko realizes that she's been putting her own desires ahead of his safety. When she discovers that Makoto ends up at the garbage disposal room, she risks her life to save him. Kyouko then showed her scarred hands to Makoto, which is a great sign of trust from her, as she states that she shows her hands only to people she considers as close as family.
During the last Class Trial, Makoto was the one who told the remaining students (including her) to not give in to despair, helping her overcoming her state of shock over the intense pressure of the situation they were in. Kyouko told Makoto that even though she didn't know her dad, he would never tell her to stay in the school if it meant betraying and getting him murdered by Junko, thus showing their bonds and trust to each other. At their "Graduation," Kyouko told Makoto she was actually kind of looking forward to face whatever is out there if it's with someone like him, hinting that she possibly has romantic feelings for him. After joining Future Foundation, she becomes Makoto's leader. Kyouko continues to admire his optimism, and Makoto in turn admires her 'cool' personality and considers her the person who has kept him alive.
In Danganronpa 3, it becomes much more evident that the two have feelings for each other, especially notable in Makoto's shyer behavior and tendency to blush more often. During the collaboration game of Danganronpa 3 and Guns Girl Z, when Kyouko is accused of being so stoic that even Makoto can't find her cute, he then a bit shyly but firmly points out that he does in fact find her quite cute, which surprises her and makes her blush. During the killing game, when Makoto overhears Kyouko talking about him with Mitarai, Makoto blushes, embarrassed by Kyouko's small speech while Kyouko coughs awkwardly after realizing he heard her. At one point, Kyouko takes off her gloves and holds his hand to comfort him, and Makoto is also seen mimicking Kyouko's thinking posture at one point. In the Otomedia magazine, Makoto states that Kyouko reminds him of autumn due to being cool as well as possessing a really warm and gentle side. He then gets very nervous and defensive about the subject and tries to change the subject by stating that coincidentally her birthday is in October. This only makes it even more suspicious, and he claims he remembers her birthday because they're friends, yet he fails to remember his other friends' birthdays. Aoi also appears to be very much aware that the two like each other, grinning widely after Kyouko's speech and later looking at the two while smiling knowingly, seemingly supportive of them.
After him trying to protect the Remnants of Despair, Kyouko has to escort Makoto to his trial and she promises to use her powers as his leader to protect him. At one point during the Final Killing Game, Makoto catches Kyouko talking about him with Ryota, which seems to embarrass her a bit and makes Makoto blush. Later, Kyouko ends up triggering her NG code of passing the fourth time limit with Makoto alive. It is possible Kyouko did not tell him because she believed he might sacrifice himself for her, and it's also possible she didn't know with full confidence that Seiko's Antagonist drug would be able to save her life completely. Instead, Kyouko gives Makoto words of encouragement before they fall asleep, telling him to never give up on hope and that she would always be by his side.
After he was brainwashed, Makoto hallucinated the "ghosts" of Kyouko and Sayaka, as he believed that she was dead at the moment. Sayaka's ghost has been confirmed to represent his first love, implying that Kyouko is his current love.
The two reunite after the Killing Game and it is implied she helps Makoto run the rebuilt Hopes Peak Academy after the events of the Danganronpa 3: The End of Hope's Peak High School/Side: Hope. In the official art, they've seen holding hands while wearing their new clothing, heavily implying that they became a romantic couple, considering their pose and the fact that the two are shown to be the type of characters who hold hands only in special situations (especially Kyouko).
The official Danganronpa 3 Staff Book confirms that after everything they've been through, the two are officially in a romantic relationship with one another as they watch over their new school.
Alternative and Ambiguous Continuities
- While not necessarily 100% canon, many of Kirigiri's optional Free Time events contain very shippy Naegiri moments from Kirigiri blushing and giggling at Naegi's personality and conversation topics to Naegi openly calling Kirigiri's smile "cute" to Kirigiri out and out asking Naegi if he's interested in "singing up" to be her family! (Complete with Naegi's iconically flustered stammering)
- During an interview Otomedia had with the Danganronpa 3 cast, Naegi was asked who comes to his mind when he thinks of autumn. This was his response: “Um…. Kirigiri-san, I guess. She’s cool but also has a really warm and gentle side– I believe that’s very much like her. I-I don’t mean that in a weird way! Y-You know, coincidentally her birthday is in October… O-Of course I would remember when her birthday is. I mean, she’s a really important friend to me… Eh, “When is Hagakure-kun’s birthday?” U-Umm…. A-Ahaha! I might’ve forgotten… I think?”
- The School Mode AU of Danganronpa allows a fair share of Naegiri moments in the same vein as the optional Free Time events. During one of the interactions, Naegi and Kirigiri make flower garlands together and give them to each other. Kirigiri thinks the idea sounds pointless at first but nervously admits that she wouldn't mind doing it if Naegi promised to accept hers. They both have a really good time with it. At the end of School Mode, Kirigiri tells Naegi she wants to keep solving mysteries with him by her side, and Naegi tells her he wants to do the same thing. They both admit to wanting to become closer and looking forward to the day it happens.
- In Danganronpa: IF, Junko Enoshima gets under Mukuro Ikusaba's skin by heavily suggesting Naegi has feelings for Kirigiri several times. She also implies that Naegi had a crush on Kirigiri before Class 78 lost their memories.
- During the collaboration game of Danganronpa 3 and Guns Girl Z, Naegi blushes at one point as he mentions shyly that Kirigiri looks cute, which surprises her and makes her blush as well.
- Series creator Kodaka has confirmed that Maizono and Kirigiri appearing in Naegi's dream sequence during Danganronpa 3 are meant to represent his first love and his current love, respectively.
- Naegiri is one of only two ships to be made canon in the Danganronpa series thus far- the other being Hijirisano. It's significantly more common for ships to be left ambiguous or for one of the characters to die before the story ends.
- Incidentally, Kirigiri was originally supposed to die early on in the first game.