As the youngest son of the master of the Shimada clan, Genji was raised in the art of the sword. He trained under swordmaster Asa Yamagami, forming a friendship with her young daughter Kiriko. Although he excelled at and enjoyed his ninja training, Genji had little interest in the family's illegal businesses and spent most of his time pursuing a playboy lifestyle. Many within the clan considered the carefree Genji to be a dangerous liability, and they resented his father for coddling and protecting him. Following the clan leader's untimely death, Genji's older brother, Hanzo, demanded that Genji take a more active role in their late father's empire. Genji refused, enraging Hanzo. The tension between the brothers built to a violent confrontation that left Genji on the verge of death.

Hanzo believed that he had killed his brother, but Genji was rescued by Overwatch and the intervention of Dr. Angela Ziegler. The global security force saw Genji as a potential asset in its ongoing operations to combat the Shimada clan. As Genji's injuries left him clinging to life, Overwatch offered to rebuild his body in exchange for his help. He was put through an extensive process of cyberization, which enhanced his natural speed and agility and augmented his superlative ninja skills.

Transformed into a living weapon, Genji joined Blackwatch and single-mindedly set about the task of dismantling his family's criminal empire. When this mission was complete, he moved on to more complex duties and even took part in the notorious Venice Incident, which led to Blackwatch’s public exposure and the team’s suspension.

Genji wasn’t sidelined for long, however. Overwatch leadership encouraged Genji to continue with agent training for the larger Overwatch strike team, and he graduated alongside Tracer and Winston. His efforts in both Havana and Singapore led Genji and his squad mates to successfully apprehend Doomfist, then the highest name on Overwatch’s most wanted list. But when Overwatch fell from grace, Genji felt increasingly at war with himself—all that had transpired between that fateful night in Hanamura and his life as an Overwatch agent. For the second time, he abandoned his former life and wandered the world in search of meaning. He drifted for many years before crossing paths with the omnic monk Zenyatta. In time, Zenyatta became his mentor, and under the monk's tutelage, Genji came to see both his experiences and his cybernetic form as a gift and a unique strength.

The Shimada brothers would cross paths once again, on the anniversary of Genji’s death. In their former home of Shimada Castle, which had since been taken over by the Hashimoto clan, Genji revealed that he had survived their fateful encounter. Genji let his older brother know that he had forgiven him, but that Hanzo must walk the path of forgiving himself. Now the master of his own fate, Genji chooses to lend his skills to Overwatch once more, returning to aid a world in crisis alongside his former comrades and any who join their cause.