When cartoon writers trick or misdirect the audience.

To keep things from being too predictable or for whatever reasons, the writer will put the story together in such a way where we come to the wrong conclusion or believe something to be untrue, only to throw a curve later in the series. Some examples I recall off hand:

Silver Surfer: The first and only season of the show had Thanos trying to earn the affection of Lady Chaos who we see is a statue. Naturally we are to assume he is crazy. The script for the second season premiere would reveal that Lady Chaos is indeed a living being who was trapped in statue form by Thanos. Okay, he is mad in a sense, but not to the point where he assumes an inanimate object is flesh and blood.

Justice League: For the sake of bringing the audience up to speed, the promotions and ads contained backgroud info on the 7 main characters. Hawkgirl's story was that she pursued a criminal on Thanagar only to be zapped by a Zeta Beam, sending her to Earth. By the time Season 2 was over, we discover that the story was merely a cover as she was sent by her planet to spy on Earth.

Maison Ikkoku: Kyoko Otonashi has a dog who goes by the name of her first husband Soichiro. For the early portion of the story, we would assume that she chose to name him after her husband. The truth is, that Soichiro was the only name that the dog would respond to.
 
The Spectacular Spider-Man:

The first season led us to believe that Harry was The Green Goblin due to his addiction to Globulin Green. The finale of the second season revealed that it was really Norman all along and that he had framed his own son and enlisted the aid of The Chameleon to protect his identity.
 
Chowder episode "Brain Grub" comes to mind. Mung, tired of Chowder's stupidity, makes a dish that makes him annoyingly smart.

At first one is to expect that Chowder's newfound intelligent would drive Mung mad and try to change Chowder back to normal. Well, that sort of happened, but not before it turned into a massive forth wall break where Chowder realized that he's in a cartoon, using his new power to turn the show into an boring, educational program.
 
I probably should specify, but I meant more along the lines where the viewer is mislead for a longer portion of the show (season long to be specific).
 
Owen, Xanato's right hand man in Disney's Gargoyles.

Heeeeeeeeeeeeeeeeerrrrrrrrrrrrrrreeeeeeeeeeeee's Puck!

Although there were hints dropped throughout the season, you had to actually go back after the curveball and say 'So, that's what they were hinting at.'
 
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