Agent Bishop of the EPF (Earth Protection Force) found out that the DNA samples of the four mutant ninja turtles were stolen. It was revealed that someone had broken into their underground base in New York deactivated the security systems and took out a number of commandos.
On TV, there was a news story that shocked Bishop and the four actual turtles. President Georges Montague of Dregovia, a French-speaking country, was assassinated by a mutant turtle resembled Leonardo who wore a blue mask and equipped with twin katana. As Bishop had once fought alongside the turtles in the battle of New York against the demon Shredder, he rationalized that the turtles would not be the ones to have broken in.
Though April O'Neil began to help clear the turtles' names, VSSE (Vital Situation Swift Elimination) could give her and the turtles two days to uncover the truth about the assassination before the four brothers surrender themselves and submit to the government of Dregovia.