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The Foot Clan was founded in feudal Japan by two men named Sato and Oshi. In Volume 1 Issue 47, the Turtles and Time Misstress Renet travelled back in time to a time prior to the Foot's creation. There, Raphael met Sato and Oshi, and, not realising who they are, he taught them about Ninjutsu. After the Turtles returned to the present, Sato and Oshi decided to follow the ways of the ninja. Oshi declared: "We must never again mention the strange shelled creatures. In time, others will join us and we will become a force to be reckoned with. So just as every journey begins with a single step... we shall call ourselves The Foot."

The Foot Clan is the most feared warriors and assassins clan in Japan. Both Hamato Yoshi and Oroku Nagi were members, until one day, they fought over the love of Tang Shen and Yoshi killed Nagi. Dishonoured, Yoshi was exiled to New York City, while Nagi's younger brother Oroku Saki was adopted by the Clan and was trained to become a fierce ninja. When he was ready, Saki was sent to New York to start the American branch of the Clan. Under his leadership, it took only a year for it to become a powerful and fearsome group.

But Saki also sought vengeance for his brother, and using the personae of The Shredder, he assassinated Yoshi. Over a decade later, the Ninja Turtles challenged Shredder to a rooftop duel to avenge Yoshi. Shredder sent his Foot Ninjas to fight the Turtles, but they were no match for the Turtles and were eventually defeated. Shredder then fought the Turtles himself, and although he was a more skilled ninja than them, he was killed when he fell off a building carrying a bomb.

After the Shredder's death, the American Foot fell apart, and the Foot Soldiers begun fighting against Shedder's elite. Karai, a Clan leader from Japan, came here to stop the clan war. She enlisted the Turtles' help in this, in exchange for promising that no Foot shall ever try to avenge the Shredder again. This truce is still in effect in Volume 4 of the comic.

The Foot Clan's logo is a drawing of a left foot. Issues 3 and 4 of the new Tales of the TMNT feature a Foot mystic with magical abilities, including the power to ressurect the dead.