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Broken Saints: Chapter 22 Act 2. On top of being freaky as hell, it is also the point where all obscurity is thrown aside, and the conflict is finally given a clear focus.
Red vs. Blue fans have come to expect this from every episode 10 per season.
Reconstruction — Episode 16. Then, Episode 19.
Earlier then that, episode 12. The Teams aren't real soldiers. It was all an elaborate training simulation run by Project Freelancer, and the cast are random nobodies who have the lowest test scores in the military, and were unknowingly placed in the program to act as Cannon Fodder for Freelancers to practice on.
Recreation had a more lighthearted mood than the seriousness of Reconstruction but the finale had a major WHAM moment Washington is now working with the Meta, and he shoots both Donut and Lopez and takes Simmons prisoner.
And of course there's always Revelations episode 9 where Tex returns after two and a half seasons, and 18 Tex shoots Church, 19 Tex gets stabbed in the fucking face by the Meta, and 20 Wash joins the blues and Epsilon decides to go looking for Tex within the storage unit, knowingly trapping himself within.
Then there's the latest installment, where yet again the season finale (this time, for season 9) turns out to be a Wham Episode with the surprising appearance of Agent Carolina, previously implied to be dead.
Episode 10 of seasons 8 and 9 have both been this trope in-universe, both times introducing Tex to the characters, and then Tex proceeds to beat up some fraction of the characters, making it a double wham episode.
Season 10 both follows and subverts this pattern — sure, Tex beats up everyone, but it ends on a distinctly sour note.
The latter half of season 10 is pretty much just one wham right after another, but the final episode is enough to rival the end of Recreation: Agent Carolina is the Director and Alison's daughter, Church leaves the Blood Gulch Gang to Walk the Earth with Carolina, and the Director closes the Freelancer Saga by killing himself.
The final two episodes of Season 11. After getting involved in the civil war on the planet the crashed on, the side the Reds and Blues are fighting for starts getting overwhelmed. They decide to retreat—but Donut, Sarge and Wash get shot. Felix forces the remaining Reds and Blues to leave them behind, but Wash wakes up and then orders Freckles to seal the tunnel they were using to escape, trapping him on the battlefield. At the end, Grif, Simmons, Tucker and Caboose are the only ones left at the rebel base, it's implied that Donut, Wash, and Sarge have been captured, nobody knows where Doc is, and it turns out that Carolina is commanding Locus.
Season 12, episode 8. Tucker, Grif, Simmons, and Caboose mount a rescue operation for Wash, Sarge, Donut, and Lopez, sneak into the federal base and get to the detention center door... only for the door to open revealing their friends perfectly unharmed and thinking that they were the ones who needed rescuing.
And then two episodes later in Season 12, episode 10, it's revealed that Felix and Locus have been on the same side all along, and they've been working together to cause the deaths of everyone on Chorus. The Reds and Blues were helping with that all along and never suspected a thing. Also, Carolina and Epsilon return, as has become tradition for the tenth episode of a season.
The Final Fantasy crossover series Final Fighting Fantasy really starts to kick the plot into gear around chapter six, Epic. But emotionally, some would say the Wham Episode is chapter three, Gaiden, which was a considerable boost in storytelling style from the first two.
Dead Fantasy — Part V shows us that characters are not in fact invincible and that these are life or dead fights and not some extreme battle exercises as many people thought.
The LeBrons has an episode called "Big Game", in which Kid LeBron loses in a big basketball game because there's seconds left for it.
Email gimmicks, the Tandy 400 explodes, and Email invisibility, Strong Bad replaces "him" with the Compy 386.
Email virus, the Compy gets a virus, destroys the universe, and Bubs kills it to restore order.
Email cliffhangers, the Lappy 486 is kidnapped, starting a month-long arc leading up to Tandy and Compy being the kidnappers, then being killed for good.
Email the paper, The Paper dies of old age, and is replaced with a designated Replacement Scrappy, New Paper.
Email email thunder, it turns out Homestar had been masterminding the series all along for his own email show, which got its own spin off for a few months. The Paper comes back to life and defeats New Paper, only to immediately die again.
Hremail 3184, Strong Bad takes the series back and destroys the Lappy, which he replaces with the Compé in Compy Catalog. New Paper is killed in the crossfire.
A Decemberween Mackerel ends with the implication that Homsar dies. The fact that the website went on hiatus shortly after the cartoon didn't help.
I Killed Pom Pom, Homestar mistakes a deflated inflatable pumpkin for a dead Pom Pom and attempts to cover up his "murder". Strong Bad uses this as a chance to mess with Homestar and get some free pastries. This is all good fun until Strong Bad decides to mess with Homestar by having Pom Pom pretend to "rise from the dead" and freak out Homestar. Instead of freaking out, Homestar decides to "fight murder with murder" and use a piece of Strong Bad's costume to kill Pom Pom for real. On the plus side, Homsar turns out to have survived.
"The Stray": Weiss and Blake have a nearly episode-long shouting match regarding the Faunus, and Blake reveals that she is a Faunus and used to be in the White Fang.
"No Brakes": The heroes fail to stop the bad guys from crashing a train through the subway wall. As a result, the Grimm swarm from the hole and overrun the city.
Toon Train seems at first to be a simple collection of humorous and bizarre short animations, which have several re-occurring elements. But if you watch it at midnight (or change your system clock), you get an Easter Egg where a detective is called to his office in the middle of the night, and you have three minutes to examine some evidence regarding the "Fitzgeraldson case" (the main menu states that the character Buttglove's real name is Lance Fitzgeraldson, but this seems like pointless trivia at first). The evidence reveals that Lance was actually a professional boxer who had his career ruined after he was defeated by a newcomer (symbolized by the cow that appears several times). Lance then joined the Navy, and ended up finding the love of his life (symbolized by the sea lion in "Seal") and having a child. The challenges of fatherhood took a toll on Lance's performance in the Navy, and this resulted in the ship he was on colliding with a mine and being destroyed. Lance's wife died, but he survived and took care of his son, while slipping into insanity. His son later gave him tickets to the circus, where he was murdered with a hammer (which also appears several times in the collab). After being apprehended, Lance claimed that "the radio made him do it", and a psychiatric analysis revealed that he heard messages in song lyrics commanding him to kill his son. Try finding the shorts funny after that.