Nine and Twelve have a deep, intimate, and brotherly relationship that at times appears to transcend verbal expression. They met in an institution, as children, connected with each other and were able to concoct a plan to escape the oppressive settlement they lived at. Although Nine looks tough from outside, he acts more openly when he is with Twelve and generally acts like a big brother. Their relationship is very deep and they will sacrifice their lives for each other without hesitation. Because of everything they've been through, Nine cares for Twelve more than anything and would do anything for him. Twelve also is able to sense when Nine is having an "episode" and frequently asks Nine if he's okay. The thought of betraying Nine is something that shakes Twelve down to his core. On his part, despite Nine's emotionless demeanor, he openly expresses profound agony and grief at the moment of Twelve's death.
Nine does not care about Lisa as much as Twelve does; this is shown when he does not go to save her with Twelve. Although he acts cold and indifferent to Lisa, he does not dislike her. He lets her stay at their apartment for a while, and even though they discussed moving Lisa out of their home, they never got around doing it. He also told Shibazaki to protect her after their deaths.
Nine and Five grew up together in the settlement, and it appears from Nine's flashbacks and dreams that his relationship with Five is something that haunts him ever since he and Twelve escaped. The exact nature of their relationship is unclear, but it seems that Nine and Five were involved in some sort of "competition" or "game" that Five insists on carrying over to the present day. Five is one of the only people that Nine views as a genuine threat, as her intelligence and hacking abilities appear to parallel, if not surpass, Nine's own. It is also unclear whether Nine harbors residual guilt over abandoning Five at the settlement, or if he merely views her as a psychopathic threat to Sphinx's ultimate goal.
Although Shibazaki is at first an capable opponent of Sphinx who is wary and angered over Sphinx's theft at Aomori due to his own past, Nine and Shibazaki share a mutual respect that later grows into a pivotal exchange of trust as Shibazaki uncovers more of Nine and Twelve's past. Nine not only turns to Shibazaki to help them save Lisa at the airport, but also later refuses to speak in custody unless he can see Shibazaki first or hold a press conference. Shibazaki, on his part, grows to become more and more ideologically aligned with Sphinx after learning about their history, and later asks to see Nine in custody as he "knows [Nine] better than anyone else [on the police force.]" In the end, Nine entrusts Shibazaki with Sphinx's final goal after their deaths, and Shibazaki becomes their spokesperson to the world.