Aigis is introduced during the Yakushima event. She is the first girl that Makoto shows interest in, with a heart above his head when he sees her. Though Akihiko and Junpei lose interest upon finding out that Aigis is an android, Makoto does not seem to. Aigis tells Makoto that her purpose is to protect him, and that she wants to stand by him.
Eventually, it is revealed that Aigis wanted to be with Makoto in order to monitor Ryoji. Aigis sealed Ryoji into Makoto in order to prevent the Fall, though she did not remember doing so. As Aigis becomes more human, however, she retains her desire to be near Makoto.
During the final month of the game, the player can choose to formally develop their bond through Aigis' Social Link. Aigis struggles with her romantic feelings for Makoto, believing herself to be an inadequate partner due to her nature as a robot.
Regardless of player choices, the two end up quite close. They have several one-on-one scenes towards the end of the game. Most notably is the game's final scene, in which Makoto passes away after falling asleep in Aigis' lap. The ending song, Memories of You, is evidently about Aigis' feelings for Makoto and her heartbreak at his tragic passing.
In the film adaptations, Aigis' relationship with Makoto is a major part of his character. Makoto struggles with the fear of death and losing his friends, and his growing bond with Aigis serves as the greatest source of that conflict. Makoto wants to be close to Aigis, but he is afraid of losing her. The two have several new scenes, including a hug in both Falling Down and Winter of Rebirth.
- Makoto has a heart above his head when he first sees Aigis.
- Aigis tells Makoto she wants to be close to him.
- When Makoto gets sick, Aigis watches after him.
- Looking into Makoto's eyes causes Aigis to break free of Ikutsuki's control.
- Aigis tells Makoto that she understands the meaning of loss, because she is afraid of losing him.
- Makoto holds Aigis' hand after her fight with Ryoji leaves her damaged.
- Aigis begs Makoto not to leave when he leaves to fight Nyx, and cries for joy when he returns. Makoto smiles at this.
- In the ending of the game, Makoto falls asleep in Aigis' lap. Aigis promises to protect and stay with him for as long as he lives.
- If the player chooses to play as Narukami, Chie assumes Aigis and Makoto are dating.
- If the player chooses to play as Makoto, Aigis tells Chie that they are together. However, she doesn't seem to understand what this means, which Yukari is quick to point out.
- Aigis tells Narukami that Makoto is the most important to her, if Narukami is paired with her at the Group Date Cafe.
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