- We'll kill things, blow things up, oh it'll be fun!!
- -- Joker src
After being defeated by Batman, suddenly; a warrior from another world appears and distracts Batman, allowing the Joker to escape. He later encounters Scorpion, a warrior from the other world and fights him, but is defeated. After Scorpion leaves Lex Luthor appears and makes an offer to Joker. He later encounteers Deathstroke, Catwoman, Captain Marvel and Superman in Metropolis, which has been ravaged by Darkseid's past invasion on Earth. Captain Marvel explains that their world is merging with another, and that they must travel to Apokolips to destroy it source. Lex orders Deathstroke and Joker to go infiltrate Sonya Blade's base to retrieve the transportation device. In the way they encounter two more outwordly warriors, including Sonya. They are forced to battle, to which everyone's (and Joker's own) surprise, Joker manages to defeat both, Deathstroke then retrieves the device but is later betrayed and defeated by a power mad Joker, who admits that he doesn't care what happens to the world. He later returns to Gotham to confront Batman with his newfound powers, and is able do defeat him in hand to hand combat, but as he gloats, Batman shocks him with a taser, leaving him unconscious, presumably taking him to the Satellite Station. He is later seen with the rest of the Justice League and villains in the Final Battle in Apokolips. He states that he likes the hellish state of the already sinister looking Apokolips.
His Arcade mode ending states that he defeats everyone and takes over Gotham City, becoming "Mayor Joker". He hosts a fighting tournament where people fight to the death for his own amusement. At the end of the tournament, the victor gets to fight the Joker himself. However it is unknown if this is true.
- Kombat Rage: When their worlds merged together, certain heroes and villains became infected by something known as the "Kombat Rage" which greatly increases the physical strength of the fighter.
- Razor Sharp Cards
- Extending Boxing Glove
- Smiley Face Bombs
- Joker's Joy Buzzer
- The fatality where Joker shoots his opponent with a fake gun, laughs and shoots the opponent in the head with a real gun was edited for US consumers to lessen the violent content.
- While the DC Universe characters are gathered in Metropolis discussing the threat of Dark Kahn, at Captain Marvel's mention of Kahn, Joker looks upward and screams "KHAAAAN!" in a homage to Star Trek II: The Wrath of Khan. 
- 2 Appearances of Joker (Mortal Kombat vs. DC Universe)
- 1 Images featuring Joker (Mortal Kombat vs. DC Universe)
- 1 Quotations by or about Joker (Mortal Kombat vs. DC Universe)
- Character Gallery: Joker (Mortal Kombat vs. DC Universe)