For generations the Yagyu Clan terrorized and robbed treasures from Leung Kar temples, though they were feared assassins before the bride system was instituted among the clans. 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 attracted to gold. During one of their temple raids, two villagers, Liu Fang and Liu Chi Mei chased after two thieves 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, addressed as 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, causing it to malfunction. The robot began chasing the Yagyu Ninja away while the trio recovered the treasure.
The Yagyu were ultimately under the command of the Bride of the Rich Nights during the Clan Wars; however, the Iron King and Queen killed the Bride and took control of the Yagyu. Using the Yagyu to her advantage, the Iron Queen eventually caused the other Brides to submit themselves to her rule and ending the warring between clans. A large number of 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 approached the city, the Yagyu Clan was ordered by the Dark Egg Legion's Kommissar, 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 forces became overwhelming, and the two heroes were forced to retreat.
After that the Yagyu guarded the Eggdome alongside the D.E.L. up until Eggman`s escape, where they ran, leaped, swung and tumbled out of the mad doctor`s path. Recovering from the escape the Yagyu went after the doctor with their mistress and much of the Dark Egg Legion in pursuit. Catching up to the former despot they found Sonic the Hedgehog and Miles "Tails" Prower. Soon the hedgehog attacked, damaging most of the saucer crafts, harassing the bats until the Iron King dealt with the hedgehog. Once more Freedom Fighters appeared the clan was pushed slightly back before their mistress rallied them for another charge. Following the heroes to the city limits where they came to a halt, unable to penetrate the shield the Yagyu along their mistress, king and allies were forced to take a humiliating retreat and walk all the way back to the Eggdome. However, they would soon return and invade the city, aided by the reprogrammed "Iron NICOLE". Though a few rebels were able to escape, the Yagyu were able to capture many of the citizens, and forced them to play audience for a public Legionization to be held in the city's coliseum.
While the Iron Dominion was securing New Mobotropolis, back in the Dragon Kingdom, after Sonic and a team of Mobians-namely Monkey Khan, Tails, and Sally Acorn-who escaped New Mobotropolis convinced the Gossamer Clan to side with Monkey Khan, members of the Yagyu Clan still stationed in their homeland requested a meeting with them. Several of them then attacked the group after mistaking them for ordinary travelers and attempting to rob them, and were handily defeated before being informed of the truth. The Yagyu Lord of that area then agreed to meet with Sally and Khan, while Sonic and Tails ended up dealing with Fiona Fox and members of the Destructix who had entered Yagyu territory. The Lord brushed off many of Sally's negotiating tactics, only agreeing to break away from the Iron Dominion when Khan proposed they leave the clan system altogether and return to the regional lord rule of the past, which appealed greatly to the Lord. Unbeknownst to them, Khan did this because he knew that the Yagyu would be less efficient without the structure the clan system had given them.
Later, with his mission in the Dragon Kingdom finished, Khan and his companions returned to the city and announced to the Yagyu ninja who had accompanied the Iron Queen that their clan had broken ties with the Dominion, promising them on his word of honor. Acknowledging the customary pledge, the Yagyu Lords over those forces led their ninja out of the city, abandoning the Iron King and Queen as well as the Dark Egg Legion to their fate.
Typical Yagyu Ninja