Although not sharing any kind of close relationship with Aoi when they first met, Makoto becomes close friends with her during their time together at Hope's Peak. During one of her Free Time events, Aoi requests that Makoto act as her fake boyfriend so she can practice when she gets a real one. Their closeness is also shown when Aoi is shown feeling guilty over having executed Makoto and she seems happy when he forgives her.
As members of the Future Foundation, the two have grown considerably closer. Makoto makes sure Aoi doesn't overdo things while Aoi frequently tells him that everything is okay. When Makoto is arrested for betraying the Future Foundation, Aoi (along with Kyoko) helps defend him, and she also helps him escape from Kyosuke Munakata when the latter tries to kill him. Makoto gives Aoi hope after she despairs at the fact that they must start a new round of killing.
Makoto remains with Aoi throughout most of the Final Killing Game, and she helps him escape from Kyosuke and Juzo Sakakura numerous times. Makoto constantly relies on Aoi, and is thankful for the help she has given him. Despite this, Makoto worries for her safety, particularly when she attempts to fight Juzo despite being at a disadvantage due to her NG code.
Makoto and Aoi have been shown to understand one another when deaths or murders occur, even since the Killing School Life. Makoto's understanding of Aoi's emotional side is ultimately what allowed him to thwart her plans to have them executed in Chapter 4. During the Final Killing Game, when Kyoko supposedly dies, Aoi fears that Makoto would become reckless and hurt himself, despite Makoto assuring her that he wouldn't let their friend's sacrifice go to waste.
The two also comfort each other when these events occur. When Kazuo Tengan is murdered by Kyosuke, Aoi gives Makoto support and gives him hope just as he did her. After his conversation with Komaru Naegi, Makoto realizes that they may have reminded Aoi of her deceased brother, Yuta, who was Aoi's Captive and thus the person closest to her prior to The Tragedy. He appeared to want to comfort his friend, however he was unable to do so as they were interrupted by Miaya revealing her robotic nature.
During the Final Killing Game, some of Aoi's expressions indicate that she knows Makoto and Kyouko like each other, and she appears silently very happy for them.
After the events of The Tragedy have been resolved, Makoto, Aoi, and their fellow survivors decide to rebuild Hope's Peak Academy together.
In THH's extra mode Dangan Academy, Aoi will ask Makoto to go on a real date with her, implying that she's fallen for him after the free time events and their time spent together at the Academy.
Just like Byakuya and Yasuhiro, Makoto has a son with Aoi in the Bad Ending of Danganronpa: Trigger Happy Havoc. In this timeline, the murders have stopped after Kyoko's execution and the remaining survivors accepted living together inside the academy for the rest of their lives. Makoto and Aoi's son strongly resembles his father and even wears clothes like him, except in a child's size.
However, it should be noted that the events of the Bad Ending were soon revealed to have happened only in Makoto's imagination when he wondered what revealing Kyoko's lie would cause.
- “Good luck, Makoto! Girls like her are total pushovers when you show a little backbone!”
- — Aoi wishing luck to Makoto with Kyoko in Chapter 3.
- “Watch out, Sakura! Makoto's transformed into a wild beast! Prime Minister Wild Beast of Beastopia!”
- — Aoi after believing Makoto started hitting on all the girls around in Chapter 4.
- “It's not fair. Even at a time like this, you're so cool.”
- — Aoi to Makoto after the latter comforts her in the subbed version of the second episode of Future Arc.
Free Time Events
- Aoi – “Then... I'm still hot?”
- Makoto – “W-Well, I mean, uh... yeah...”
- — Makoto after Aoi worries about getting fat in their fifth Free Time Event.
- Aoi – “People have always told me how I'm not ladylike... And I mean, I can't really disagree. All I'm good at is sports, exercise, physical stuff... But maybe that's just because I've never actually been in love...! Since I've never fallen in love, how can I say I'm a woman? So that's why... Um... I want you to be my boyfriend.”
- Makoto – “Uh...”
- Aoi – “N-No, I mean-! Not like my REAL boyfriend! Just, like, a practice run!”
- — Aoi wants Makoto as her boyfriend for a practice in their sixth and final Free Time Event.
- Aoi – “Anyway, thanks Makoto! You've definitely helped lift that weight off my chest! And on top of that... I kinda had fun practicing with you. I might ask you to help me again someday!”
- Makoto – “N-No, I think that's enough practice for me...”
- Aoi – “Oh, really? Then... if it wasn't practice...?”
- Makoto – “Huh?”
- — Aoi and Makoto after finishing Aoi's relationship practice.
- “"Would you, go on a real date with me?"”
- — Aoi during her Dangan Academy ending.
The ship has sailed mostly as a result of the ship tease in their Free Time Events, where Aoi asks Makoto to be her boyfriend, albeit just for a practice, although it's implied that they became official if the player talks to Aoi at the end of Dangan Academy. Otherwise Makoto most likely ends up with Sayaka in that timeline. It was fueled even more with Future Arc, where Makoto and Aoi are together during the entire Final Killing Game and support each other.
- Aoi Asahina/Makoto Naegi tag on AO3
- Aoi Asahina & Makoto Naegi tag on AO3
- Naegi/Asahina tag on FanFiction.Net
- Makoto/Aoi tag on FanFiction.Net
- Aoi's relationship with Makoto on Danganronpa Wiki
- Makoto's relationship with Aoi on Danganronpa Wiki
- Both are among the five characters who have participated in two killing games, with the others being Hajime Hinata/Izuru Kamukura, Kyoko Kirigiri, and Rantaro Amami.
- Although Aoi gets a fake death from the narrative perspective, they're also among the four characters who have not only participated in but also survived two killing games, with the others being Hajime Hinata/Izuru Kamukura and Kyoko Kirigiri.
- Naegirihina refers to the ship between the two and Kyoko Kirigiri