Foot Clan
Utrom Shredder (Future Shredder | Cyber Shredder) | Karai | Hun | Baxter Stockman | Dr. Chaplin | Yukio Mashimi | Foot Elite | Foot Mechs | Amazonian Blade Bots | Shredder Clones | Foot Mystics | Mutant Foot Soldiers
Purple Dragons
Hun | Dragon Face | Johnny | Two Ton | Spike | Sunny
The Federation
General Blanque | Lonae
Triceratons
Zanramon | Commander Mozar | Triceraton All-Stars | Gruell
Battle Nexus
Ultimate Ninja | Dark Ninja Assassins | Drako | Kluh | Ammag | Levram Wizard | Slashuur
Ninja Tribunal Arc
Tengu Shredder (Shredder Tengu) | Heralds of the Shredder | Bone Demon
Others
Agent Bishop | Rat King | Darius Dun | Sh'Okanabo | Dark Turtles | Viral | Torbin Zixx | Harry Parker | Nano | Garbageman | Dr. Malignus | Black Horde | Abigail Finn | Parker | New York Mafia (Big Boss, Weasel) | Turtlebot | Texas Roughnecks | Ananda | Mr. Touch and Mr. Go | Marlin | Skonk | Ruffington | Necro Monster | Moriah | Master Sliver | Savanti Romero | Triple Threat | Mephos | Boss Zukko | High Mage | Jammerhead | Lord Hebi | King of Thieves | The Brotherhood (Councilor)