Slowly formed over the years by crime syndicates consuming and absorbing one another until there was only Yakuza, the faction has had its ups and downs over the years. Originally headed by Mikage Yukiato, the Yakuza had an extensive structure full of infamous names- the most corrupt lawyer Rajura Doji, the enforcers Amano and Arago, the great thug Rungo Naaza, the cunning scientist Dr. Jennifer Cain, and Mikage's secretary Yuri Higashi.
In addition to this, there were several tools the Yakuza had to enforce their will. Chief among these were the Shadow Hunters, elite androids led by Gimel and Zayin. There was also the Loath family, including Glyde Loath and Lex Loath. They were frequently assisted by the Bonnes and the Red Dragon Striders. In the early years of the Robot Masters, they enjoyed an alliance of mutual benefit with the Yakuza, the Yakuza serving as the Robot Masters' chief supplier of arms and supplies while Dr. Wily provided the Yakuza with technology (such as the robotics training necessary to build the aforementioned Shadow Hunters) and the promise of immunity from his own rampaging army. In later years when the Robot Masters became self-sufficient, the Robot Masters increasingly ignored this promise and the alliance became increasingly strained as a result. The Yakuza later forged on-again off-again alliances with Neo Arcadia.
However, the Yakuza became stagnant after some years. A Yakuza mob boss named Sera rising in the ranks seized power after the assassination of Mikage Yukiato by an unknown party (Sera herself having a solid alibi), also placing in high rank her personal translator and bodyguard Geetz. Sera began to shake the Yakuza up, but to many, it felt like it was being shaken apart. Many of the Shadow Hunters escaped due to loopholes in their programming, going solo. Sera brought in several of the scattered tribes of Africans, and posing as a businessman, stole the secret of Power Armor from Dr. Deo Darrius. Sera and her loyal supporters assisted in the removal of many of the old guard of the Yakuza, and Amano and Arago were killed. Rajura Doji jumped ship and sold a massive list of Yakuza agents to Interpol, ravaging the crime syndicate as many arrests were made. The Yakuza also lost their expert hacker Techno, whom Shadow Man convinced to join the Robot Masters.
Sera Mwozoki abandoned the Yakuza to ally her Triads directly with Grandmaster Meio. The Yakuza has still not fully recovered from the many blows they have taken over hte years.