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The son of the Daimyo, the Ultimate Ninja first came to Earth to fight Oroku Saki, The Shredder. However, he was deprived of this chance after learning that The Shredder had seemingly met his death at the hands of Leonardo. In response, The Ultimate Ninja challenged Leonardo to a mortal duel, and the two fought. The duel was intense, and neither could the gain the advantage on one another for a lengthy period of the battle. The Ultimate Ninja managed to throw Leo over a bridge assuming that Leo would fall to his death. However, the turtle survived, climbed back up, and managed to defeat The Ultimate Ninja with relative ease. The ninja then dishonorably attempted to kill the turtles and Splinter (who were spectating the battle) by conjuring up a dragon, which the Daimyo sliced in half, after the fight ended. The Daimyo appeared from behind a cloud of dust and saluted Splinter for teaching his sons such honorable ways of fighting.
The Ultimate Ninja appeared again later when the Turtles entered the Battle Nexus. Allied with the evil Drako, a former rival of Splinter's, he planned to destroy the Turtles and take over his father's throne and the multiverse. He nearly succeeded by both poisoning Leonardo and implicating Splinter in an attempt to murder The Daimyo. However, the Turtles, along with their allies, Miyamoto Usagi and Traximus, were able to thwart his plans. Both The Ultimate Ninja and Drako were then pulled into a rift in space and time created by Drako's nefarious use of the Daimyo's War Staff.
He later appeared as a pet of Savanti Romero, having been fused with Drako into a grotesque entity known as The Ultimate Drako. Stealing the Time Scepter of Lord Simultaneous, he scattered the Turtles throughout different realities, captured Splinter, and weakened his father, The Daimyo. He later seized the War Staff after Leonardo failed to use it to recover his missing family. Wielding the power of The Scepter and Staff, he gathered Leonardo and Usagi together, trapping them in a battle with powerful monsters.
With the Turtles occupied, Ultimate Drako was ready to destroy The Daimyo. But some part of The Ultimate Ninja still partially cared for his father, and his hesitation allowed Splinter to grab onto The War Staff and summon his sons to him. The Turtles and Splinter managed to gain possession of the two relics. The Time Scepter, being partially sentient, combined its powers with those of the War Staff to restore everything to their natural order, including the separation of The Ultimate Ninja and Drako. However, both were then petrified and crumbled to dust. Fortunately for the grieving Daimyo, Lord Simultaneous decided to give his son a second chance, and revived the Ultimate Ninja, bringing him back as a child.
The Ultimate Ninja later befriended the Turtles when they returned to the Battle Nexus for Michelangelo's rematch to determine the true victor of the Battle Nexus tournament. He remembered Leonardo, but decided that he must have been someone he played with and declared him his friend. He was temporarily held hostage to ensure that The Daimyo could not interfere with the removal of the Nexus' safety rules, but rescued by Leonardo. Later on, he and his father witnessed April's and Casey's wedding from the Battle Nexus through an interdimensional window.