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The Ultimate Ninja is the son of the Ultimate Daimyo, the master of the Battle Nexus which is a tournament from the greatest warrior every three years to see who is the champion of the multiverse.
The Ultimate Ninja makes his first appearance in "Ultimate Ninja." He came to Earth to challenge the Shredder but learned that the Shredder met his apparent demise by Leonardo. So he challenged Leo to a duel and they fought to the death. However, the Ultimate Ninja fought with no honor and tried to kill Leo after the duel was finished.
However, despite this, he has a caring side for his father to the point of banishing him to an unknown island instead of killing him. By the time he and Drako are separate beings once again, he begs his father to forgive him before being turned into stone. Luckily, he is revived as a child with no memories of his actions.
Dark Ninja Assassins worked for Drako and the Ultimate Ninja in the 2003 TV series. Drako first used them to attack Splinter after he lost a Battle Nexus match to him. But Splinter was assisted by Miyamoto Usagi and the Ultimate Daimyo, who chased Drako and his assassins off with his War Staff. Later Ultimate Ninja used them to try to kill Leonardo. The Ultimate Daimyo blame Splinter and install the Ultimate Ninja as Damiyo.
Same as it Never Was - TMNT Film (Read Description)