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KateModern: Precious Blood, in which Lauren is abducted, the team discover a top secret Order base, the killer is (at last!) revealed to be Terry, Steve's faith is tested to breaking point, Steve and Charlie kiss, Gavin leaves for Manchester and the Watcher dies.
Season 2, Episode 7 "Tempest" of The Leet World. Leeroy is kicked off the show, the box from Noonian is revealed to be a Red Herring planted by the Producer, and a video message from Leeroy reveals that the Noonian scientists have all been killed, and that the Producer has been dead for five years.
In the Whateley Universe novel "Christmas Elves", at the end of chapter 2, team sweetheart Jade Sinclair (The Chick) is stabbed through the heart while Fey is unable to stop it. Since this is a comic book world, she gets better. But then the cute kid of the team goes psycho and murders dozens of Mooks to rescue herself and Fey. And it's hilarious.
AH.com: The Series: the first season ending episodes "Of Ships and Captains" and "Once More Into the Breech", which suddenly showed the very serious back-story that led, years in the past, to the current largely comedic rambling adventures of the battered old ship and crew — and then those events return to haunt them...
Episode Nine of There Will Be Brawl. Zelda stabbed Link and left him for dead, Bowser sacrificed himself so Luigi can escape his castle, and Red was killed in an explosion.
Before that, Episode Seven was very whammy as well: Link didn't sanction the raid on Dedede, Red got arrested too, Kirby knows who the butcher is and ESCAPES FROM HIS CELL, Mario took on the whole police force, the other characters are finally aware of Zelda/Sheik's dual identity, and Captain Falcon incinerates Isaac and Saki with a Falcon Punch, Big Damn Heroes fashion. Your jaw was on the floor, admit it.
The end of the current chapter of the Union series. Up until this point, the main characters have been fighting a grey war, until at the end of their current assignment they discover they will either directly or indirectly commit Xenocide.
Marble Hornets: Entry #26 Alex is alive and still stalked by The Operator, Entry #49 Alex kills a man and leaves his body for The Operator, and Entry #61 We witness how Tim becomes his masked persona.
Seeking Truth: Inside the Labyrinth Zeke encounters the Slender Man and Lizzie is killed
Tribe Twelve: "HELLOTHERE" and "COMECLOSER" Videos from the Observer, Nature Trail Visit Noah encounters the Slender Man and blacks out for a week., November 11th We see who the Observer truly is, and Mary Asher Phone Call Milo's mom reveals she's been stalked too, and that Milo's body went missing.
Everyman HYBRID has "Healthy Eating" The HYBRID crew encounters the real Slender Man after realizing it isn't their friend Daniel in the fake suit, Joke's Over The crew realizes they're not being pranked and abandon the fitness aspect, One step forward, two steps back The Rake attacks Evan and murders Alex's dog, and The property Dr. Corenthal is still alive.
The Secret Life Of Dolls' "Paradise Lost". Edward Tallen makes good on his claims that he's dangerous, and kills Ellowyne Two.
"Tandy Computer Wiz Kids: Fit To Win #1": Linksano is leaving, not because of a previously teased Mechakara, but because multiverse conqueror Lord Vyce is coming, and after playing him up reveals that he's headed this way. Then Linkara disappears in a flash of light and isn't heared from for AN ENTIRE MONTH.
"Silent Hill:Dead/Alive #'s 5 and 6": The Magic Gun is actually an ultra powerful weapon created in a nightmarish ritual using th e soul of an innocent girl. Said girl narrowly saves Linkara from committing suicide by speaking to him allowing him to win. And then to top it off we see Lord Vyce in full view for the first time and learn he's brought in a specialist... Linksano.
"Spider-Man: Planet of the Symbiotes" reveals the true identity of The Entity. It's MissingNo using the image of 90's Kid
The "Youngblood #4/Star Trek III" double feature reveals the intruder wasn't Mechakara, it was Lord Vyce.
The Spoony Experiment (AT4W's sister series of sorts): Let's Play Final Fantasy X part 3. Black Lantern Spoony is intent on taking the show back and is bringing back the one person that can help him do just that, or to put it more accurately: TIDUS OF ZANARKAND, RISE!.
Also, the finale of his Ultima retrospective. It started off light and cheery, but as the series became more and more unloyal to his childhood fandom, (the series that introduced him to RPGs and videogames in general) The end of the Ultima IX review betrayed his childhood to the point where he tosses the box into a wall offscreen, went on a long open rant about how the series had fallen, and he looked and sounded like he had literally been broken.
During the finale of his review for Final Fantasy XIII, he knows full well someone from the game is gonna fight him. It ends up being Snow, who proceeds to beat Spoony bloody before Spoony can get the upper hand on him and rip his throat out. No wisecracks or remarks were made after the fight.
The The Nostalgia Chick has Kirk VS Picard, which includes a legitimately unexpected twist: they actually had the balls ovaries to kill off BFF Nella! (Though it looks like she will be coming back — as a quasi-demonic intergalactic force of evil, no less).
Another episode plays it for laughs when, after Angry Joe shows up and reveals that the next review will be of Man of Steel, the Critic lampshades that now they don't have a cliffhanger, only for Mr. Zebub to run in:
'Mr. Zebub: I'm pregnant
An unexpected one occurred during Chapter III of The Insane Quest of Unfathomable Randomness: Oh, look, a Quirky Miniboss Squad made up of cloned versions of the heroes. They'll probably just be thwarted by the end of this Chapter and then everyone will forget all abou- Wait, did one of them just kill Nico? Well, didn't see that coming. I guess these guys aren't so harmless after al- Wait, now everyone else is dead too? Son of a-!
In New Prime, we have New Prime 4. The gate of lost gates leads to The White Void, revealing that it is in the same universe as The Last Scene, it's revealed that Dutch was Killed Off for Real by The Phantom, Daniels was Ferris' brother, Ferris meets Valavingee, and Bob was revealed to be The Phantom in disguise, as he takes the medicines from Ferris. Talk about Cerebus Syndrome.
Agents Of Cracked's aptly titled The Plot Twistingest Finale in the History of Final Episodes. Ready? Okay. *deep breath* Spoilers abound: Michael is the Chief's son. Cracked was created entirely to keep Michael busy and hidden, because if the other Chiefs found out there was a "retarded demi-god" running around, they would kill him. T-Bone was a security robot, but he turned on the Chief and leaked Michael's existence to the others. Broked is staffed entirely by doubles of the Cracked team (the Chief invented cloning), including B-Tone, who has been reprogrammed to kill Dan and Michael. There's a secret code on Cracked.com that reveals the secrets of the universe to anyone who reads every single word on the site and buys certain items of Cracked merchandise. Michael has been subconsciously weaving the code into all of his articles. Also, as of the last thirty seconds, he and Dan are a couple.
The next episode is little better with us finding out that Lewis Brindley and Simon Lane were very nearly correct in their joking assumption that they shouldn't accept milk from a suspiciously cheery barkeeper, who went on to become an important, more developed character in the series... and who was about to kill himself when they met. He would've killed them too out of paranoia if he hadn't decided to risk them not being possessed by the ultimate evil.
And the episode after that deals yet another Wham:
Knight Peculier tried to swim in lava.
The Yogscast's Yog Labs series as well, with the episodes Soul Absorber and Clone Lab. The series started out as a clever way to show off mods, but quickly escalated until the story took over. In these two episodes, two Yog Labs employees rebel, which ends up with Simon's master clone—essentially his ticket to respawning—dead. Without it, if he dies, he's dead permanently. In order to keep his respawning ability, Simon takes his place, even though Lewis tells him he'll lose all his memories. After a surprisingly touching goodbye, Simon is frozen in the cloning vat, and Lewis walks away...and we zoom in on a robot back in a corner with the sign "Nothing Lives Forever" on it. Holy. Shit.
In Marriland's Pokémon Emerald Nuzlocke, episode 15, "In Shock and Awe!", his starter, Waffles the Combusken, is killed against Wattson, from a critical hit against his Magneton no less. Devin defined losing his starter as the defining changing point of the series, in comparison to other Nuzlockes where the players still have their starters intact very late in the game.
The story "'Verse Chorus" in Fine Structure introduced us to the Imprisoning God, who 1) won't let Mitch leave the universe, 2) regularly changes the laws of physics, and 3) kills Mike, Seph, and a plane full of people.
Part 8 of TGWTG's To Boldly Flee is a big one, with many Wham filled moments, but two stand above all the others in it. When tHE Nostalgia Critic enters the Plot Hole and finds out that he's just a character, talking to Doug Walker himself. And Critic's final fate, to becoming one with the Plot Hole to save his friends and the world.
The Season 6 finale of Red Panda Adventures, There Will Be Rain Tonight. Most of the Red Panda's agents are missing behind Nazi lines, most of the Home Team is killed, and the Red Panda and Doc Rocket's plane explodes in flight.
Episode 7 (out of 18) from Season 3 ; it turns out that Fantöm's avatar has been illegally enhanced for several years and get arased along with all its accomplishments. The damage eventually gets mostly repaired, but it takes the rest of the season.
Up to three quarters of Season 4 episodes can qualify, making it a Wham Season. It started with the Season 3 issue partially resolved and the status quo seemingly coming back, but ended with Arthéon's mind snapping, Omega Zell in Justice and apparently there to stay, Gaea in the Coalition and Noob guild disbanded. Each of these situations required two or three consecutive status quo changes.
And then in Episode 32, Old Woman Josie's angel friends disappear, the Man in the Tan Jacket is given several possible names... and StrexCorp moves into Night Vale, buying the radio station.
In Episode 33, Cecil discovers a set of cassette tapes he made from when he was fifteen and shares them with the audience. Teenager!Cecil rambles about his family, the state of the town and his internship at Night Vale Community Radio. Except Adult!Cecil doesn't remember making the tapes. Nor does he remember anything about interning at NVCR, whatever it was that was following him at the time, or even having a brother. This episode also includes the first reference to Cecil's last name, something the fandom had previously assumed he shared with his voice actor.
Episode 36, Missing, revolves around Tamika Flynn's sudden disappearance and StrexCorp's attempt to hunt her down and capture her. Cecil may or may not have severed all ties with Strex after they threatened to shut down his show and is hiding on the roof of the Night Vale Community Radio Station, urging his listeners to revolt. Since this is likely the lead in to the live episode airing sometime in December, this is sort of a given.
You purchasing the "One Mind" upgrade in Cookie Clicker. Before that, everything's played as Black Comedy at worst. From that moment on, as the tooltip helpfully tells you, it's alldownhill.
Tokyo Magic Star: Episode 5. The villains come from Hell itself, and the girls aren't just warriors, but blood sacrifices as well.
Episode 5 of TOME. The first season finale could count as this as well. These episodes firmly acknowledge that The Forbidden Power, which had previously been a valuable asset to Alpha, is a VERY big bad.