Typical Yagyu Ninja

For generations the Yagyu Clan terrorized and robbed treasures from Leiling Kar temples. They would stash their stolen treasure in an underground lair near their Haunted Lake base. The treasure was guarded by a "dragon," a giant green robot that is attracted to gold. During one of their temple raids, two mobians, Liu Fang and Liu Chi Mei chased after two ninjas until Monkey Khan engaged the ninjas. The Yagyu members used smoke as a distraction while they escaped. Monkey Khan, Liu Fang, and Liu Chi Mei traveled to their hideout where they were ambushed by many Yagyu ninja. The leader of the group, Lord Yagyu, dropped the trio into the treasure room, where the robot dragon began to attack them. The dragon only focused on Monkey Khan because of his gold Power Ring headband, but Monkey Khan damaged the robot. The robot began chasing the Yagyu Ninja away while the trio recovered the treasure.

It is unknown what happened to Lord Yagyu but the rest of the clan followed the Bride of the Rich Nights during the Clan Wars. The Iron Queen killed the Bride of Rich Nights and took the Yagyu as her own. The remaining clans also started following the Iron Queen. The Yagyu Clan accompanied The Iron Queen, the Iron King and the Bride of Conquering Storm to New Megaopolis where Snively, Dr. Eggman's "nephew," declared the Iron Queen the new ruler of the Eggman Empire. They searched with Conquering Storm through the ruined city for anything working or of use, but found the Eggdome to be the only operational part of the city.

When Sonic the Hedgehog and Monkey Khan ambushed the city, the Yagyu Clan was ordered by the Dark Egg Legion's Kommisar, Lien-Da to fight them off while they stayed in a safer position as support. They proved to be formidable opponents against Sonic and Khan, especially when assisted by the Dark Egg Legion troops. After the Iron King joined the battle, the Yagyu helped win the battle, and the two heroes were forced to retreat.