The Foot Clan is an ancient ninja clan, led by the Shredder and operating out of New York City. During the events of Batman vs. Teenage Mutant Ninja Turtles, the Foot Clan's influence spread to Gotham City, as the result of a deal between Shredder and Ra's al Ghul. Shredder's goal was to obtain a Lazarus Pit, and thus allow the Foot Clan to rule for a thousand years.
A large number of Foot Clan ninja were sent out to obtain advanced technology from laboratories across Gotham, which attracted the attention of both the Ninja Turtles and Batman. For the duration of Shredder and Ra's al Ghul's alliance, the Foot worked alongside the League of Assassins to defeat the joint efforts of the Turtles and Batman.
In order to keep their enemies from reaching Ace Chemicals, a large number of Foot ninja were mutated in order to fend off intruders.