Oroku Saki's younger brother Kazuo Saki works for the Tokyo Metropolitan Police force, and parts of the episode My Brother, the Bad Guy are set here, where Shredder breaks into the Ninja Hall of Fame.
The Hamato Clan was headquartered in Tōkyō, and was where Hamato Yoshi lived with Tang Shen and Miwa. After the Hamato Clan was betrayed and destroyed by Oroku Saki (the Shredder), the new Foot Clan was also established in Tōkyō, and was the primary headquarters of Foot Clan operations until the Shredder moved to New York City to hunt down Yoshi. Miwa—renamed Karai—also grew up in Tōkyō.
In the film Out of the Shadows, Baxter Stockman is taken to the Foot Clan's facilities in Tokyo.