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Adventures in Odyssey is largely a realistic show about realistic small-town problems, frequently more comedy than drama. It had a few forays into serious territory early on, whether it was an adaptation of a Bible story or a robbery... but when Dr. Blackgaard showed up, things changed.
The Cult of Apophis in Yu-Gi-Oh! East Academy presents a very real and significant danger to the heroes; their appearance marks the darkening tone of the RP.
New World Order. They debuted in one of wrestling's most cartoony eras and proceeded to utterly annihilate every face who stood in their way. They were led by Hulk Hogan, formerly an Invincible Hero, now a cruel and vindictive heel who loved to play the numbers game. Hell, they were so dark that Sting went through a personality 180 from a cheery surfer from a brooding Crow-type just so he could effectively combat them!
The Undertaker's Ministry Of Darkness. They crucified and hung their enemies, kidnapped women, brainwashed midcarders, made blood pacts in the middle of the ring... only infighting and The Undertaker getting injured put an end to them.
The Nexus made their debut by savagely beating down everyone around the ring- and we mean everyone. The faces, the heels, the trainers, the announcers, the commentators... they even destroyed the ring! Wrestling/RAW ended with the seven of them standing tall, everything around them utterly annihilated. And it got worse from there.
The Wyatt Family. With the WWE's current Lighter and Softer atmosphere, it's really jarring to see a gimmick like this one, especially considering it may be one of the most disturbing and genuinely unnerving characters in the history of the company.
The Shield. While they've started to fall apart in 2014, they debuted as a brutal SWAT Team-like trio who would steamroll anyone with flawless teamwork and then Triple Powerbomb them through a table.
Randy Orton. It's easy to forget that, prior to the summer of 2007 when he really began to establish himself as a main-event heel, WWE had for months and months been a carnival of kooky gimmicks: evil cheerleaders, a leprechaun, a "monster" who ate worms, Booker T thinking he was a medieval king, Mr. McMahon getting his head shaved...Even the (kayfabe) destruction of Mc Mahon's limo and Chris Benoit's (real-life) death earlier that summer couldn't quite put a damper on the silliness. Then Orton loses his title bout against John Cena at SummerSlam, pouts about it...and, after Jonathan Coachman tells him that he hasn't "proven himself" yet, kicks Cena's father in the head just to guarantee that he'll get a rematch.
Makuta from BIONICLE started out menacing enough, but his constant defeats and failures gradually robbed him of his credibility. After the original head of the Story Team left, the character of Makuta underwent a serious retcon, which resulted in him turning into a calculating mastermind who had planned his victory from the start, turned out to be the Bigger Bad behind a lot of former villains, and by the end of the story arc, ended up winning.
Noob is set in a MMORPG, so the early villains, while annoying and sometimes geunine threarts in-game, were no longer a problem once characters logged off. Then enter Master Zen, who has a deep resentment against the protagonists and is willing to go after them in real life. A plot present in all three incarnations of the franchise included him breaking into one of the protagonist's appartement, while the webseries had him resort to kidnapping and the comic showed outright (but fortunately failed) murder attempts. Even this wasn't enough for Stupid Good Sparadrap who still thinks of Master Zen as his former Guild Master, so his own storyline has Roxana: she become the first player he geuninely hates after she kills his pets and he eventually gets her to break out of her But for Me, It Was Tuesday attitude towards the incident, which causes her to hate him back.