Some TMNT stuff really isn't for little kids.
Bruce Wayne is a billionaire playboy socialite who is secretly a superhero known as Batman.
As a boy, Bruce Wayne's parents were murdered by Joe Chill, who attempted to steal his mother's pearl necklace. Since that fateful day in Crime Alley, Bruce from then on decided to avenge his parent's deaths by fighting crime and injustice that plagues Gotham City.
Batman is contacted by a scientist who works at Powers Laboratories, and tells the Dark Knight about a break in there. She describes a battle between the Foot Clan and the Turtles which resulted in the theft of an experimental generator. Batman vows to find the stolen tech, then returning to the Batcave, he tries to uncover the perpetrators. He is able to deduce that both teams of assailants were skilled in the art of Ninjutsu, thanks to the scientist's description of the fight. His friend and butler, Alfred Pennyworth believes that the League of Assassins to be behind the burglaries, but Batman did not. The way the clan of ninjas moves does not match the League's modus-operandi, so he is quick to reject that theory. Also there have been more thefts in Gotham City by these ninjas, all of which seem to be components to building something.
Batman then decides to stake out a Wayne Enterprises R & D facility because it is the next likely strike for the ninjas. Using some kind of hologram machine, Batman is able to fool the Foot Clan with false images of scientists who work there. The Batman demands they give him the reason they have been stealing all this equipment. A fight broke out and the Batman was victorious against the ninja clan. He interrogated one of the ninjas, who told Batman they merely "trying to get home". Batman then demanded to know about their metahumans, which confused the ninja. He tried to explain about these "turtles", but before he could, the ninja was killed by the Shredder, who warned Batman to stay out of his way or Gotham would pay the price.
Later atop a roof top, Batman witnessed the Turtles and their master Splinter gathered around his car and suddenly he realized what the Foot ninja meant when he mentioned turtles.
Batman confronts the Turtles in a one on four battle against them, which Leonardo and his brothers were not prepared four. The Batman was able to put up a tremendous fight against the four Turtles. He took out Raphael first by disarming him of his Sai, then used the Batmobile's long ranged tase cables. Then Michelangelo attempted to avenge his fallen brother, but Batman easily defeated him and used Mikey's own Nunchaku to defeat Donatello. Leonardo, with his two swords in hand attempted to defeat Batman himself and avenge his brothers, but Batman used Raphael's Sai to break one of Leo's swords. Batman then attempted to gather information about the break in from Leo, which he assumed the Turtles were a part of.
Leo tried to explain that they only meant to stop it, but before anything was learned Splinter leapt in between them. Splinter and Batman had a short fight too and their Sensei admired Batman's skill in martial arts. However he tossed a smoke bomb which allowed them to escape from Batman.
Back at Wayne Enterprises, Batman as Bruce Wayne with Lucius Fox examine Raphael's Sai. Lucius explains to Bruce that the Turtles are from another universe. He explained the theory was from one of their scientists who was earlier kidnapped. Doctor Naveen Khan had begun the possible construction of a trans-dimensional portal, a way to cross into other dimensions. Also that the small amounts of mutagen that created the Turtles on the Sai is beginning to become inert. Which Bruce deduced the Turtles and Master Splinter will revert back to their original forms before mutation. They then discuss that all the missing tech along with Doctor Khan's kidnapping, someone wishes to build such a portal. The only missing component was a "resonance engine". So Bruce explained to Alfred about the Turtles and his need to find the engine before the Foot Clan can. Then he dons his costume to his the streets then seek out the Turtles and Splinter. Who in fact was watching what Batman had said about he and his sons. So then Splinter with his sons leads them to Batman's place of business, the Batcave.
Totally Awesome Team-Up
Batman encounters the Turtles and Splinter in the Batcave after Alfred alerts Bruce that there are intruders in the Batcave; there is a small skirmish with Leonardo and Raphael. Batman demands to know how they entered his cave and Donatello ends up telling Batman about a small flaw in his security. Something which seemed a bit irrelevant to Batman, but then Master Splinter surprises Batman by revealing he knows Batman's true identity. While shook, he and Splinter to speak to one another and he learns why the Turtles and Splinter have arrived in his universe. Then of course both mention the fact that if they do not leave Batman's universe soon, they will no longer be mutants and revert back to their original selves.
Batman decides to help the Turtles and Splinter, but before they make their move, Alfred confronts Splinter and his sons with a shotgun. Batman orders Alfred to stand down, then tells Splinter about Shredder's machine and that he vows to get the Turtles and Splinter home.
The united force then storm Penguin's Iceberg Lounge, where Batman rescues Doctor Khan. He tells Khan to head towards the dock where Alfred was waiting for him. With him safe, the Turtles and Batman fight their way through Shredder's Foot Ninja to get their way to him. The battle looks won for the heroes, but Shredder plays his trump card by destroying the portal and had planted a bomb in Khan's head, that killed him. Unimpressed with Batman's reputation, the Shredder makes a get away, but not before he injures Raphael in his right shoulder.