When he was younger, he was somewhat tricked into selling his legs to Kanno. His legs were replaced with Texhnolyze legs that allow him to hear the 'voice of the city', which are visions the Mothers send to him about things that will happen in Lux.
Most of the main council of Organ had some kind of qualm with Oonishi, first and foremost being his passive nature. Even on the battlefield, he prefers to not kill his opponents. In the office, he believes in talking things over first before starting an unnecessary war. This causes a number of the council members to try and oust him out of office.
First was Mizuno, who used Yoshii's interference in Lux's affairs to place blame on Oonishi for being too conservative. He gets his wishes and has Oonishi on the run after the large skirmish between Organ, the Alliance, and Lakan. Soon after, his wife is taken hostage by Yoshii and is killed in a skirmish. With the help of Touyama, he uncovers Yoshii's plot and manages to save Goto and Class Dude from being assassinated before being gashed across the chest by Yoshii. Ichise saves him and he is eventually able to recover.
While he was recovering, Mizuno's plot was also uncovered due to Touyama and Ichise's detective work and he was reinstated as leader of Organ. He goes and visits the Elder of Gabe, who was a long-time ally of Organ, to see if anything can be done about the current disarray of Lux. The Elder has him listen to Ran's prophecy in which she tells Oonishi that 'what you lost is coming to destroy you', insinuating that Kanno will soon arrive. While there, he uncovers Gabe's new alliance with the Class and is betrayed a second time by Mizuno. However, he is saved from being killed by Ichise.
He takes Ichise under his wing around this time. He realizes the potential that Ichise has and wants to try and get him to focus it on things other than blind rage.
He is then betrayed by Kohagura, who has made an alliance with Kanno, and loses his position as head of Organ. After having Ichise save Goto from the Shapes and guiding a losing battle against some shapes with the Alliance, he heads off to the gate to try and talk to the Class. He is let in by the Mothers who then tell him who Kanno is and his plans for taking of Lux and using the Shapes to take over the Class. They tell him that he has to warn the upper world about Kanno's plans.
Instead, he returns to Lux and asks Doc to tell the upper world because he believes they will be more receptive to her. He asks Ichise to go with her, but tells him that his debt is repaid.
Along with Shinji, he gathers the men of Lux up in order to oppose the Shape forces. Under his leadership, they're able to ultimately win a very bloody battle with their enemies, though at the cost of many, many lives.
He ultimately arrives in front of the Obelisk and asks the voice of the city (Ran) what he should do to stop the madness. Ran asks him to kill her and he obliges. He drives his katana into the Obelisk, which bleeds, and is then shot apart by an angry mob of anti-Organ / anti-Texhnolyze men.