Batman arrives via glider at Metropolis Harbor. He is met by the Joker and a LexCrop Spider Bot.
Meanwhile, Superman uses a lifeboat to weld over the whole in the side of the cruise ship.
At the harbor, Batman engages as Spider Bot. The Joker escapes while the robot pursues Batman into the streets Metropolis. Eventually Batman arrives at the Daily Planet looking for Clark. He finds only Lois. The Spider Bot soon arrives and attacks Batman. Eventually, with the help of Lois, Batman sends the robot into a printing press. Batman, however, is unmasked in the process. Lois sees that Batman is really Bruce Wayne. Before she can have words with him, the Spider Bot attack them again. Superman, however, arrives in time to save them.
At LexCorp Headquarters, Luthor realizes that wreckage from the Spider Robot can be traced to him. He tells Mercy to arrange a final meeting with the Joker.
At her apartment, Lois tends to Bruce's wounds. She expresses her frustration at him over his secret identity. As Lois heads out for some iodine, Superman arrives. Bruce thanks Superman for saving him. Bruce says that he can link the robot to Luthor. The two agree to a partnership.
When Lois returns, Bruce is suiting up as Batman and is preparing to leave. He leaves before she can tell him to be careful.
Meanwhile at LexCorp, Joker and Luthor discuss business. Luthor wants Joker's Kryptonite. When Harley reveals that they brought it, Mercy pulls a gun on them. Luthor plans to pin the wrap wholly on the Joker. Unfortunately, the Joker turns the tables on him. He knocks Mercy out and Harley takes the gun. The Joker kidnaps Luthor and steals a powerful LexCorp flying wing.
Superman and Batman arrive and enter Lex's building. The Joker activates several Spider Robots as a distraction. He sends them after Batman and Superman and takes off in the flying wing.
After a short fight, Superman and Batman manage to dispose of the Spider Robots. They manage to free Mercy who was tied up to one of the machines. She tells them that the Joker has kidnapped Lex and that he wants to destroy everything that Lex has ever built. Superman is worried when he realizes that Lex built most of Metropolis.
Batman heads off to stop the Joker while Superman stays behind to deal with the final spider robot.
Meanwhile over the city, the Joker attacks LexCorp buildings throughout Metropolis. Eventually Batman arrives and engages them in the Batwing. Using the LexWing's missiles, the Joker shoots Batman out of the sky. Batman manages to escape and jumps onboard the LexWing.
At the same time, Superman fights off the Spider robot even after it exposes him to Kryptonite. Using a lead lined door Superman smashes the robot and sends it flying right out of the building.
The Joker continues to attack the city when Batman attacks him and knocks him off of the controls. Harley takes over and begins to crash the aircraft. Superman arrives just in time to stop the ship from crashing. The Joker and Batman fight until the Joker reaches for his exploding marbles. He drops the bag causing small explosions all over the ship. Batman grabs Harley and Superman grabs Lex. The two of them escape the LexWing before it explodes. The Joker attempts to get a parachute. Unfortunately the LexWing tilts and knocks him to the ground. He sees the exploding marbles heading his way and he laughs hysterically. After a few moments, the LexWing explodes and crashes into the ocean.
Superman flies over and grabs Batman and Harley. They head back to the city with Lex in tow.
Later, Angela Chen reports that the Joker's body has not been found. She also reports that the D.A.'s office has been questioning Lex over his connection with the Joker's rampage. She also announces that Bruce Wayne has cancelled his partnership with LexCorp and that Harley is being taken back to Arkham Asylum.
At the airport, Bruce and Lois talk. She tells him that she can't go with him and heads off. As he heads to the plane, Bruce runs into Clark. Bruce wishes him good luck with Lois and heads off.