WARNING: This section contains heavy spoilers for Dangan Ronpa 1, Dangan Ronpa 2, and Dangan Ronpa 3.
Makoto Naegi and Kyoko Kirigiri first met upon being scouted to join Hope's Peak Academy's 78th class. Naegi was selected as the Ultimate Lucky Student by winning a random nation-wide lottery, and Kirigiri was selected as the Ultimate Detective by showcasing her history of solving numerous extremely difficult criminal cases. Not much is known about the first two years of their relationship because those memories were wiped from their minds by Junko Enoshima, along with everything else that happened around that time.
Roughly two years after meeting each other, they met again as unwilling participants in Monokuma's Mutual Killing Game. Naegi was initially shy around Kirigiri, and Kirigiri was initially distant due to her near-universal distrust of people and the life-threatening reality of Monokuma's game. Their relationship began to change after Sayaka Maizono was killed in Naegi's dorm room. While the majority of Class 78 suspected Naegi of killing her, Kirigiri's experience as a detective allowed her to deduce his innocence very early in the investigation, and throughout the first trial, she acted as Naegi's ally in order to lead the class to a correct verdict. When questioned as to why she did not simply solve the case immediately and bring the trial to an early end, Kirigiri explained the she felt Naegi's only hope of moving on from Maizono's death was to reach the truth himself. This gave Naegi a positive opinion of her early on and would act as his driving force in protecting and forging a legitimate friendship as the game progressed.
Throughout the course of Monokuma's Killing Game, Naegi would turn to Kirigiri for advice during investigations and trials while attempting to gain her trust during free time. Kirigiri was not always open to Naegi's advances and would often keep him at a distance for fear of showing her cards to a possible killer (or even the mastermind). This would lead to a few personality clashes between the two, as Naegi was naturally open and trusting, while Kirigiri was naturally closed and suspicious. During one particularly nasty clash, Naegi successfully convinced Kirigiri to tell him about a secret room she had been investigating on the second floor but later refused to tell her about a suspicious conversation he overheard between Monokuma and their fellow classmate, Sakura Oogami. This resulted in Kirigiri refusing to talk to Naegi for several days straight or even be in the same room as him in several instances! They made up for the disagreement later and Kirigiri visibly blushed while admitting to her overreaction.
Naegi and Kirigiri's relationship throughout Monokuma's Killing Game can be described as "unique" and "constantly evolving" with respect to both characters. Naegi is generally supportive of all his classmates and wants to protect all of them, but he shows unusual amounts of support and concern for Kirigiri. Kirigiri is distant and distrusting of everyone, but she shows unusual amounts of reliance and trust in Naegi. By the third case in the game, Kirigiri is willing to ask Naegi for his personal assistance in investigating the crime scene and filling her in on the details when she is late, despite the still present possibility of Naegi himself being the killer. In that same case, Naegi is vehemently hostile toward suggestions from other classmates about Kirigiri being the killer or a possible spy for the mastermind. Byakuya Togami notices Naegi's unusually protective attitude and suggests Naegi might be in love with her, resulting in a weak and stuttered denial from the Ultimate Lucky Student. During the fourth case, Naegi and Kirigiri openly operate as partners during the investigation, apparently trusting each other enough to simply believe neither is the killer without any need for strict evidence. Around the same time, their classmates also picked up on how close the two were and made frequent comments about it, some of the most suggestive occurring when the two had their afore mentioned disagreement about sharing private information. Most of the class assumed that their falling out was related to romance problems.
Perhaps some of the most defining moments in their relationship occurred before and during the fifth trial of Monokuma's Killing Game. Before the trial- in fact, before a body was discovered at all- Kirigiri used a master key she had stolen from the headmaster's office to sneak into parts of the school Monokuma was not monitoring. She enlisted Naegi's help in distracting Monokuma to do this (again showing inordinate amounts of trust in him), and Naegi only agreed to the plan on the provision that Kirigiri promised she would come back alive. Just in case, she entrusted him with a sealed envelope that supposedly contained her final thoughts. Monokuma was none the wiser and even teased Naegi for his mysterious late night conversations with the girl he had obviously grown very close to. Once Naegi's distraction was complete and the mastermind noticed Kirigiri had vanished, they attempted to set up a trial that would frame Kirigiri for murder and have her executed. The initial plan involved killing Naegi in his sleep to accomplish this feat, but Kirigiri discovered the mastermind sneaking into his room and briefly fought them off to make sure Naegi would stay safe. When the inevitable trial did come around, Kirigiri and Naegi were the only two suspects due to the false nature of the crime, and they were forced to argue back and forth between which of them could have killed the victim. When it came down to the wire, Kirigiri was the last one to insist she was innocent, and Naegi willingly sacrificed himself to execution, despite having evidence that could incriminate Kirigiri. Naegi believed in Kirigiri thoroughly, even when the evidence suggested she could be the killer, and it was only through luck that he managed to survive the following execution and fall into the school's garbage dump. Kirigiri rescued Naegi a couple of days later and expressed sincere regret to him multiple times for the way things turned out before finally opening up completely and revealing everything she knew about herself.
Naegi and Kirigiri worked together to escape Monokuma's Killing Game and free the surviving members of Class 78 from Hope's Peak Academy. When they faced the mastermind together and it was revealed that the outside world was an apocalyptic wasteland, Naegi gave Kirigiri the hope to continue moving forward and leave the school with everyone else. In response, Kirigiri promised to never leave Naegi or abandon him again, and right before stepping outside, Kirigiri told him that she felt she could live in the world no matter its state, as long as someone like Naegi was there with her.
Naegi and Kirigiri's relationship continued its positive- though mostly platonic- growth throughout the next few years of their lives until they were roped into Monokuma's Final Killing Game, along with 13 other members of the Future Foundation. Prior to this event, Kirigiri was appointed as Naegi's supervisor and the two appeared to have a productive working relationship. Kirigiri expressed to Aoi Asahina that she would do anything she could to protect Naegi when he was under investigation by his superiors, and she willingly risked her life to help him rescue the Remnants of Despair by entering the Neo World Program during a completely unauthorized mission.
During the Final Killing Game, Kirigiri saves Naegi's life very early on by blinding the room with a fire extinguisher so he could escape the moment people started getting aggressive towards him. She later volunteered to save Naegi when he had been taken captive by Kyosuke Munakata, but Kazuo Tengan steped in to do it instead. After she determined how the killings were happening, Kirigiri insisted on finding Naegi to report to him, claiming he was the strongest person in the Future Foundation and absolutely crucial to stopping the Final Killing Game. Naegi overheared her saying this and developed a nervous blush. Kirigiri tried to play off her awkward yet sincere expression of emotions with a cough.
The mastermind had assigned Forbidden Actions to each participant in the Final Killing Game, and violating them would result in death by poison for the violator. Aware of the close relationship between Naegi and Kirigiri, they made sure Kirigiri's Forbidden Action was "Surviving past the fourth time limit with Makoto Naegi alive", and Kirigiri intentionally violated this action without warning Naegi for fear he would do something rash. It is heavily suggested that Naegi would have voluntarily killed himself if he knew what Kirigiri's Forbidden Action was. Instead, Kirigiri removed her glove and held Naegi's hand during their final meeting before the fourth time limit. She encouraged him to never give up on hope, told him how much he meant to her one last time, and promised to always be by his side right before time was up.
Naegi was devastated by Kirigiri's apparent death, but after crying profusely, he used it to motivate him into confronting Munakata and ending the Final Killing Game. During said confrontation, Naegi successfully trapped Munakata in a room and forced him to talk things over. He used his experiences with Kirigiri to relate to Munakata's angst and fear over his dead girlfriend and explained how he felt the situation should be dealt with. Ultimately, Naegi's feelings for Kirigiri and the history of their relationship allowed him to break through Munakata's enraged nature and reach a compromise. When Munakata accused Naegi of loving Kirigiri during their fight, he did not deny it or even challenge it.
After the Final Killing Game ended, the Remnants of Despair were revived, and the Future Foundation began to recover, Naegi's last thoughts during the events were of Kirigiri and how much he would miss her. Fortunately for him, she had actually found a way to subvert the poison that was injected into her earlier with a carefully laid out plan, and Kirigiri reunited with Naegi outside of the Future Foundation HQ.
Several month later, the two would go on to rebuild Hope's Peak Academy and staff it with trusted friends and family to lead the world into a brighter future. Naegi is currently operating as Hope's Peak Academy's Headmaster, and Kirigiri is working happily by his side. The official Dangan Ronpa 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 Dangan Ronpa 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 Dangan Ronpa 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 Dangan Ronpa: 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 Dangan Ronpa 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 Dangan Ronpa 3 are meant to represent his first love and his current love, respectively.
- Thus far, Naegiri is one of only two ships to be made canon in the Dangan Ronpa series. The other being Takumi Hijirihara x Mekuru Katsuragi. 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.