When the 1988 Shredder rescued Ch'rell the Utrom Shredder of the 2003 Teenage Mutant Ninja series, Ch'rell immediately overthrows his bumbling other-self and seizes control of the fortress with the aid of his adopted daughter Karai who had been monitoring his movements and tracked him down after realizing he had escaped his frozen prison.
Ch'rell and Karai noticed that the 1988's Foot robots were clumsy and weak, even cartoonish. Karai, using Utrom technology upgrades the Foot robots into the Foot Soldier Mark II which would become the new Foot Ninja replacing Ch'rell's human Foot soldiers who would later be upgraded into mutants to increase Ch'rell's army.
The new Foot Soldiers were fast, tough and very deadly. They were so advanced that they almost killed the 2003 Turtles and 1988 Turtles. They are later used in Ch'rell invasion of New York. When Ch'rell leaves New York in the upgraded 1988 Shredder's Technodrome the Robotic Fott soldiers quickly shut down as the Technodrome sent out all signals to them.