It's a dark and stormy night in Gotham City as the owner of an Antique Shop is about to close up, but then a mysterious woman enters, allegedly to trade in a music box. It then springs open to reveal a jester head and douses the man with some gas, which turns out to be Joker venom. Joker then unmasks her to be Harley Quinn and enters to steal a green dragon statue, claiming that he may just have use for it.Later, the police investigate the crime scene and wonder why Joker would only take one jade statue, worth maybe a hundred thousand dollars, especially when rumor has it that he's short on funds. Batman examines a fragment of the statue that had been left behind and takes it for further study.
Back in the Batcave, he runs test on the sample, while Alfred reports that the "Laughing Dragon" has gained a bad reputation for being cursed, since all of its owners died prematurely. Batman knows why: the "jade" is emitting low-level radiation, meaning it's actually Kryptonite. Now realizing what the Joker is up to, Batman heads off to Metropolis, where, incidentally, Bruce Wayne has business to attend.Out over Metropolis, terrorists seize control of Air Force One, with the President of the United States on board. Lois Lane is among the press corps on board, virtually guaranteeing Superman's prompt arrival. He easily defeats the terrorists and saves the passengers. When he returns to the ground, Lois tries to let him know how she feels, but they are interrupted when robbers attack the First National Bank, and Superman must fly.
Lex Luthor sourly reads about the President thanking Superman and calls Mercy to get his car ready. Suddenly, she is knocked out by a mechanical Boxing Glove. Luthor enters the car and orders Mercy to take him to the office. However, the driver is revealed to be not Mercy, but Harley Quinn. Luthor then attempts to escape, but Harley locks the car and speeds off, driving quite recklessly. She then notices "a cute hitchhiker" on the edge of the street, which is the Joker lifting his pants leg. She brakes to a halt and the Joker enters the car, explaining to Luthor that he is broke, thanks to Batman's success in closing down his operations in Gotham City. So he makes Luthor an offer: for one billion dollars, he'll kill Superman. Luthor is initially skeptical as he wonders how the Joker has any chance at beating Superman when he can't beat the less powerful Batman. He then changes his mind when the Joker shows him the Kryptonite statue. After the Joker assures him that it couldn't be traced back to him, he accepts.
Later at the airport, a group of reporters, including Lois and Clark are awaiting the arrival of Bruce Wayne, who is revealed to be in Metropolis to oversee a cooperative venture between Wayne Enterprises and LexCorp. Lois reveals what she has heard of Bruce, believing him to be "Gotham Trash". However, Lois is immediately taken with him when he steps off the plane, as he is arriving Lois is checking herself until she is surprised to see Bruce behind her referring to her as the famous Lois Lane. Flustered, Lois accidentally bumps into him while dropping her belongings.
Lois then begins to pick up her belongings while introducing Clark to Bruce. However, he ignores Clark and instead helps Lois, revealing he was impressed with her adventure on Air Force One. Lois then asks him what brings him to Metropolis, however they are interrupted by Mercy who informs Bruce his car has arrived. Bruce then invites Lois over dinner to discuss the news and Lois happily accepts Bruce's invitation, much to Clark's displeasure.
That night, the Joker sets up his base in Metropolis, gassing a local crime boss, Ceasar Carlini and taking his hideout and his cowered thugs for his own. Carlini is later found, hysterical with laughter, by the Metropolis police, alerting Superman to the Joker's presence in the city. The next day, an insect-like probe droid, the Wayne/Lex T-7, crawls through a canyon even scaling walls. Bruce is pleased at how well his and Luthor's companies have collaborated in developing the robots for space exploration. Luthor says the robots would be even more useful for military purposes, but Bruce, who under their agreement has sole control over the technology's uses and more so with his hatred for guns, firmly squelches the idea.
Later that night, Bruce and Lois are enjoying their date, where Bruce is asking about Superman. Lois then teases him saying does she need to fix them up together. Bruce apologizes but Lois instead apologizes for her remark, where she admits she was hoping to not talk about Superman, revealing how she has been "consumed" with him lately. Wanting to take her mind off and enjoy the rest of their date, Bruce and Lois enjoy a lovely dance, thus blossoming their romance.
Later on, Batman appears in a Metropolis nightclub, finding a runaway thug from the gang Joker recruited. While Batman is interrogating him, Superman arrives, saying he doesn't want Batman's brand of vigilantism in his town. To his astonishment, Batman throws him across the room with a judo move. Superman strikes back by ramming him into a wall, which allows the thug to escape. Using his x-ray vision, Superman peeks behind the mask and sees that Batman is Bruce Wayne. Batman then pulls out the Kryptonite fragment and warns Superman of the Joker's plan.
Superman returns to his apartment. His jealousy increases when he gets a call from Lois, who says she's taking the morning off to have breakfast with Bruce. As they talk, he notices a small, bat-themed homing device planted on his cape and picks it up. Clark goes to look out his window, as Lois hangs up. He uses his telescopic vision and spots Batman on the roof of a distant building, watching him through binoculars. Clark realizes Batman has now discovered his secret identity as well and crushes the device in anger.
Things don't start off very well between Batman and Superman. Lois and Bruce flirt with each other at the Daily Planet, much to Clark's chagrin. But out of her earshot they talk about Joker's location, and Clark drops a warning about Bruce's relationship with Lois, which he dismisses. Revealing he and Lois are now in a serious relationship and points out to Clark that he missed his chance with Lois. Lois then returns and she and Bruce leave for their date, while Clark is left more annoyed and jealous.
The night over dinner at a rooftop restaurant, Bruce and Lois are getting closer, but Bruce a bit concerend asks if there is anything between Lois and Clark. However, Lois assure him that his only competition "flew away sometime ago". Bruce and Lois are just about to share a kiss until they are interrupted by the sudden arrival of the Joker. Bruce and Lois are surrounded by Joker's thugs. Joker then leaps at Lois and shocks her with his electric buzzer, leaving her unconscious in his arms. Bruce demands he let Lois go and attempts to rescue her, but the thugs begin to shoot at him and he soon falls over the edge. However, Bruce manages to save himself, however they contuine to shoot at him, until Bruce begins to fall again. Bruce then soon grabs an edge of the hotel. Joker is soon in his blimp where he rides off with a kidnapped Lois.
Later, the police and Superman have been alerted of the event and assure Bruce that Lois will be saved. Bruce and Superman share a private talk, where Bruce informs Superman to expect the unexpected from Joker, however Superman dismisses his warning and flies off. At Joker's hideout, he and Harley show a tied up and gagged Lois the Kryptonite statue, where he breaks it in half, saving one half for later. Harley takes off Lois' gag where she expresses her disgust of the Joker's plan. Harley then gags Lois again. Joker then tells Lois that she has the story of the century in her hands: The Death of Superman.
At a LexCorp storage unit, Batman (having secretly brought the Batwing with him) flies off into the sky to rescue Lois. At Metropolis Police Department, Joker contacts Superman, inviting him to come alone to one of LexCorp's laboratories. Batman tracks Superman's location and starts to follow him. Superman arrives at the laboratory wearing his Anti-Kryptonite suit. Joker appears confused when the Kryptonite has no effect on him, and Superman quickly gets him to lead him to where Lois is. But just as Superman is about to save Lois, Joker uses his acid flower to destroy the suit. Exposed to the radiation, Superman is quickly defeated by Joker, and who gleefully celebrates his victory by electrocuting Superman with his buzzer. Before he can kill Superman, however, Harley Quinn calls and warns that Batman has arrived. Joker leaves, and as soon as Batman enters the room, the doors are sealed and Joker Gas is vented in.
Batman examines the room's contents: barrels of hydrochloric acid, too weak to eat through the walls or door, but instead, Batman uses it to dissolve the Kryptonite. Recovering from its effects, Superman is just able to smash their way out of the room, taking Batman and Lois with him. They confront Joker, who distracts them with grenades made to look like marbles. They flee the laboratory, which is destroyed in an explosion.
The next morning, Luthor makes a public statement that the explosion was only a minor problem but is furious with Joker for destroying his property. Clark, among the reporters, hears Luthor mention of his deal with Joker. Later at Joker's hideout, Harley tries to cheer him up, but Joker is furious over what had occurred the night. Suddenly, they are attacked when gunshots start to appear out of no where, while Joker and Harley hide for cover. They soon stop and the intruders are revealed to be Luthor and Mercy, Luthor confronts Joker and is furious at him using one of his laboratories.
Joker then calls out to Harley, while Luthor calls out to Mercy and a fight soon ensures between them. As Mercy and Harley fight, Luthor and Joker talk, Luthor demands an explanation and Joker reveals to him that Batman has arrived in Metropolis. Luthor is shocked, but Joker assures him that he still has half of the Kryptonite and can finish the job. However with Batman now involved, Joker demands more money, Luthor refuses saying that if he can't handle Superman or Batman than their deal is off. Luthor then calls out to Mercy alerting her it's time they leave and warns Joker that he has one last chance.
Later, Clark arrives at Lois' apartment, wanting to check up on her, however he is surprised to see Bruce there and attempts to leave. However, Lois stops him and asks to at least tell her why he stopped by, Clark then reveals to Lois and Bruce of how he believes that Luthor is involved with the Joker, but can't prove it yet. Bruce then offers to help stating he could "ask" Luthor.
In his apartment, Luthor is rudely awakened by Batman. Batman demands to know what deal has he made with Joker, Luthor denies anything as Mercy sneaks behind Batman and attempts to attack him, however already realizing her presence Batman knocks her unconscious. He again asks Luthor, who refuses to tell him anything. They are soon interrupted when they hear more of Luthor's bodyguards, as Batman leaves he warns Luthor that he'll be back. Luthor's bodyguards bust in, but find Batman gone and are about to ask what happened but re told by Luthor to leave. Mercy then awakens and is told by Luthor to call Joker, who realizes that Batman is a serious enough threat and that he must be taken care of as well. Lois tells Clark that she's planning a transfer to the Planet's Gotham City bureau, feeling that she and Bruce are serious enough that they're practically engaged. Clark is upset from the news, however they are soon interrupted when Perry alerts them to a distress call from a cruise ship. While Lois starts to immediately work on the story, Clark sneaks away and flies off as Superman. At his hotel, Bruce is working out until he notices a blimp sent by the Joker, inviting Batman to Hobbs Bay. Bruce is confused at to what the Joker is up to now, Alfred then appears with his uniform and the Jet-Wing and Bruce as Batman soon takes off.
Superman arrives at the cruise ship and asks the captain what is the problem. However, he is confused and both him and Superman find a fake a distress signal near the ship to lure Superman away. However the distress becomes real when a bomb is detonated on the hull, causing the ship to sink. Batman arrives at the dock, where he meets the Joker, but it turns out to be a trap as Batman is attacked by a now armed Wayne/Lex T-7.
Out at sea, Superman repairs the damage to the cruise ship and prevents it from sinking. At the same time, Batman flees the Wayne/Lex T-7 using his new Jet-wing until the machine damages it. In desperation, Batman heads for the Daily Planet building to find Superman, but he is not there, and Lois happens to be doing a late night.
With her in danger of being caught in the crossfire, Batman snatches her up and together they try to run. They are cornered by the robot in the printer room. As it tries to push him into the press, his cape and cowl are caught and pulled off, revealing his identity to Lois. She manages to distract the robot from killing Bruce, long enough for Superman to arrive and destroy it. Luthor is informed of the Wayne/Lex T-7's failure and realizes that he'll be connected to the crime. He decides to cut his losses and orders one more meeting with Joker.
Back at her apartment, Lois treats a wound on Bruce's shoulder. She is fuming because Bruce deceived her, and also because she honestly cares for him enough that she can't release the story of Batman's true identity. Superman arrives and asks Bruce for a partnership so that they can take in both their enemies. Batman agrees and they leave.
Meanwhile, Joker and Luthor meet at a LexCorp aeronautics factory, where Luthor informs Joker and Harley that he intends to kill them and frame them for all the mayhem that's been going on. Joker turns the tables and takes both Luthor and Mercy prisoner. Since he can no longer collect his billion dollars, Joker decides on a "consolation prize": Luthor's gigantic and heavily armed Lexwing airship (having Harley paint it so that it resembles a grinning mouth, as it is built in the shape of a crescent moon). Luthor offers to pay for his release, but Joker says he isn't interested in money anymore. Instead, he wants to destroy everything Luthor built. Batman and Superman arrive but are attacked by giant versions of the Wayne/Lex T-7's before they can stop Joker from taking off. Working together, they destroy most of the robots, but then are faced with one that has Mercy strapped to its side as a shield, preventing them from hitting it. Batman manages to get the robot off the ground and Superman deactivates it without hurting Mercy. Mercy tells them of Joker's plans, which Superman realizes means destroying half of Metropolis. The group is confronted by a larger, more advanced robot. Superman tells Batman to go after Joker while he takes care of the robot. Unfortunately, this one is equipped with the other half of the Laughing Dragon, rendering Superman unable to fight back.
Joker goes on a destructive spree over Metropolis. Batman pursues in the Batwing. Joker damages the plane with missiles, and Batman is forced to eject, but manages to board the plane. While Batman deals with the wing, Superman is pummeled by the robot until it tries to smash him with a heavy door. The door, which had been lined with lead to block Superman's x-ray vision, protects him from the Kryptonite and he destroys the robot, in the process shattering the last of the Kryptonite to pieces. Superman heads off to help stop the Joker.
Batman confronts the Joker, leaving Harley to fly the wing, but she only succeeds in shutting off its engines. Fortunately, Superman arrives just in time to steer the wing away from a collision with a building. In the fight, Joker accidentally drops his entire bag of marble grenades while going for his gun. As the grenades start to explode, the heroes save Luthor and Harley but are unable to reach the Joker in time. As the Joker goes for a parachute, he is trapped by the grenades rolling towards him. In the face of death, the Joker starts laughing maniacally. The grenades go off, setting off an explosion, destroying the wing as it crashes into the ocean.
With the troubles over, Angela Chen reports on the incident: Joker's body has not been found. Luthor is under investigation, but it is unlikely he will be charged with any crime. However, Bruce Wayne, discovering that Luthor has been developing military versions of their robots, terminates his deal with LexCorp. Harley is returned to Arkham Asylum, much to the amusement of a beaten up Mercy, who is watching her public arrest on TV and enjoying the last laugh at her expense.
Sadly for Bruce, Lois says she adores him, but can't get over his secret activities. He said goodbye, and he and Clark exchange a well-intended farewell before Bruce leaves for Gotham, leaving Metropolis and Lois in Superman's care once again.
- Ash Ketchum, Pikachu, Misty, Togepi, Brock, Molly Hale, Littlefoot, Cera, Ducky, Petrie, Spike, Ponyo, Sosuke, Scooby-Doo, Shaggy Rogers, Fred Jones, Daphne Blake, Velma Dinkley, The Sailor Scouts, Annoying Orange, Peat, Apple, Passion Fruit, Midget Apple, Marshmallow, Grapefruit, Grandpa Lemon, Nerville, Princess Sapphire, Choppy, Discord, The Human Mane 5, Sci-Twi, Spike the Dog, D-Team, Alpha Gang and their Dinosaurs, The Tenkai Knights (Guren, Ceylan, Chooki, Toxsa, Gen and Beni), The Bakugan Battle Brawlers and their Bakugan, The Grand Duke of Owls, Kurumi Tokisaki, The Dazzlings, Bowser, Mistress Nine, Bowser Jr., Granox, Slyger, Attila and Hun, Oakley and Annie, Cassidy, Butch, Dr. Facilier, Grizzle, Spectral Space Pirates, Darla Dimple, Broccoli Alien Overlord, and Team Rocket guest stars in this film.
- The Grand Duke of Owls, Kurumi Tokisaki, The Dazzlings, Bowser, Mistress Nine, Bowser Jr., Granox, Slyger, Attila and Hun, Oakley and Annie, Cassidy, Butch, Dr. Facilier, Grizzle, Spectral Space Pirates, Darla Dimple, Broccoli Alien Overlord, and Team Rocket will work for Lex Luthor and The Joker in this film.