This game takes place during the ending of Justice League Task Force in which a defeated Darkseid escapes to another dimension in search of the Anti-Life equation in which he would use it to dominate any and all universes. Upon learning it is in the dimension he escapes to he makes it his sole mission to find it there. However the very dimension he finds himself in is a parallel universe in which he and all others are seen as comic book characters and nothing more. This very place is populated by the Teenage Mutant Ninja Turtles.