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In "Game Over for Owlman", Batman's archenemy teamed up with the Caped Crusader to defeat Owlman when the villain was upstaging his own crimes. He joined Owlman when he gave him an opportunity to kill Batman at last. During the fight, he and Owlman ended up trapped in wax. As Owlman was returned to his dimension in bondage, the Joker alongside the other bad guys were sent to prison. The Joker did comment that he enjoyed working with Batman before being loaded into the paddy wagon, restrained in a fashion similar to Hannibal Lecter in The Silence of the Lambs. In "Legends of the Dark Mite!", the Joker makes an appearance as an illusion in the 5th Dimension. He was bowled over when Batman bowled Tweedledum and Tweedledee into the villains. He appears again in "Hail the Tornado Tyrant!" where he is being tailed by Batman and Green Arrow. He was defeated by the combined efforts of Batman and Green Arrow. He also makes a cameo at Arkham Asylum in "Mayhem of the Music Meister!". The Joker appears again in "Death Race to Oblivion" and "Chill of The Night."
He also featured as the main villain in the episode "Emperor Joker" a partial remake of the "Emperor Joker" storyline in the comics in which he acquires Bat-Mite's limitless powers and uses them to reshape reality in his image. However when he is tricked into entering Batman's mind he finds himself in a world were Batman doesn't exist, meaning he is sane, and relinquishes his powers to escape.
He appears again in the episode "The Knights of Tomorrow!", which was entirely a fiction story written by Alfred Pennyworth where an aged, dying Joker trains a new successor in a plot of revenge against Batman.
He reappears in "Joker: The Vile and the Villainous!" which shows the world through his eyes and shows that he and Batman are very much alike. He helps villains and crooks and they look up to him the same way Batman does with heroes. He foils Batman's plot to make Gotham safer but was sad when Batman saved his life. He reappeared again in "Night of the Batmen!".