The Ninja Tribunal are a group of four Ninjutsu masters who were trained by special Mystical Ninjutsu Masters. They would later go on to recruit acolytes over the centuries, to whom they teach the hidden secrets of ninjutsu so they can help prevent the return of the Tengu Shredder.
Each of the four Masters represent Spirit, weapons, strength and Stealth.
During the early fourth century, the people who would become the Ninja Tribunal, as well as a human Oroku Saki, were Japan's five greatest warriors, who rose to fame after they, under the order of the Emperor of Japan, slayed a feared tengu called The Shredder. They became known as "The Five Dragons".
However, Oroku Saki who killed the evil Shredder had infact made a deal with the demon. The Demon offered him power, Saki accepted this and the Demon went into Saki and Oroku Saki would become known as the Tengu Shredder. Now imbued with the Tengu's power, Saki began a reign of terror throughout Japan, aided by a demon army along with his Foot Mystics.
The remaining four Dragons would then train with Mystical Ninjutsu Masters from around the world, gaining knowledge and power. With their physical and mystical power vastly increased, the four heroes engaged Oroku Saki in battle in order to bring an end to his tyranny. After finally defeating Saki in their dragon avatars, the four warriors knew that the Shredder could not be destroyed - his evil magic was too great. So, they imprisoned Saki in a cask, and hid the three artifacts; his helmet, gauntlet and body. If the three artifacts were to be united, the Shredder would rise again. They have since kept constant vigil over the artifacts, recruiting acolytes such as a Ninjutsu Master known as the Ancient one.
The Ancient One's student, Hamato Yoshi, came to the Tribunal to ask for their aide to defeat the Utrom Shredder called Ch'rell an alien criminal, but the Tribunal refused, as the alien was not the true Shredder they simply saw him as a alien bug, even dismissing Yoshi's concerns that Ch'rell may challenge the original Saki. This ignorance led to Yoshi's death at the hands of Ch'rell. After Splinter the mutated pet rat of Yoshi brought back Yoshi's ashes to Japan, the Ancient One informed the Tribunal of Yoshi's passing but they were unconcerned. Unknown to everyone, the Ancient One was followed by a bone demon, sent by the Foot Mystics to locate the Shredder's objects. But the young Turtles were able to see through the cloak and damaged the amulet that hid him, allowing him to be defeated. The Tribunal admired the Turtles' prowess but erased their minds and sent them back home. They would later choose them to be Acolytes. With the Foot Mystics' release from Karai's grasp the adopted daughter of Ch'rell, the Tribunal made their move to train the new Acolytes and secure the Shredder's artifacts. But once all of them were at the Lap of the Gods, the Mystics obtained them, seemingly destroyed the Tribunal.
However, the Tribunal taught their acolytes a lesson that everything they know about the world, themselves and about reality itself would be challenged and secretly allowed their Acolytes to live, watching how events unfold. When the Shredder was defeated, the Tribunal appeared, explaining that by causality, by not helping the Utroms, it created Splinter and the Turtles. Now that their duty is done, they prepared to "move on" and invited the Ancient One to join them.
The Tribunal later attend the wedding of Casey and April the friends of the Turtles and Splinter. At the wedding the Cyber Shredder and the Foot clan attack. The Tribunal help defeat the Cyber Shredder.