Nagi, and Shizuku seem to have a very good relationship with each other. Nagi is her friend, and they seem to be close to each other, as Shizuku does not care if Nagi believes himself to be a girl, and as Nagi doesn't care if Shizuku is in love with her own older brother, in fact he encourages it. It is also stated, by Ikki, Shizuku usually never gets close to anyone, especially someone of the opposite sex, so for Nagi and her to have such a relationship is truly amazing.
Nagi and Shizuku's relationship is proven even greater then just a simple friendship as Nagi sees Shizuku as his little sister, something that he hasn't felt in a long time. Nagi cared so much for Shizuku that he was willing to betray the very man who took her in.
Nagi and Ikki have a friendly relationship, and Nagi describes Ikki to be exactly as what Shizuku made him out to be, kind.
Although Nagi and Stella haven't interacted much they seem to have a friendly relationship.
Nagi and Kagami seemed to have a really strong relationship with each other as they seem to always gossip and talk every day. However this seemed to be a façade by Nagi, who seems to think very little of the girl even willing to kill her at a moments notice without any hesitation whatsoever.
Nagi seems to be very loyal to Wallenstein after the incident with the government and their hiring of the local thugs. After which Wallenstein had taken Nagi in and Nagi and him had began a student master relationship with each other.
However Nagi's relationship with Wallenstein does not seem to be a loving one but something derived out of fear of Wallenstein, knowing how powerful Wallenstein is, Nagi dare not encourage Wallenstein's wrath.
Yuuri was Nagi's dear friend during their childhood. They were both orphans, who looked over other younger orphaned children. Nagi and Yuuri were almost complete opposites, with Nagi being very calm and full of gentleness, while Yuuri was lively and full of unyielding spirit. Yuuri's death was a very traumatic experience for Nagi, and a major reason for Nagi joining Rebellion.