The two part episode "Two Face" from Batman: The Animated Series. Harvey Dent had already been established as a good, loving man at this point, and you're rooting for him every step of the way to not become a bad guy. Hedoes.
"Heart of Ice". Not only for taking a joke villain like Freeze and turning him into a legitimate threat, but was the first time a cartoon show ever seriously delved into themes such as vengeance and that characters could die.
These were the bread and butter of Transformers: Beast Wars, especially in the second and, to a lesser extent, third seasons.
A heavy one was the Death of Dinobot, who has an entire episode dedicated to his Dying Moment of Awesome where he takes on the entire Predacon lineup including the Implacable Man Rampage and, as far as he knew, stop Megatron's plans of changing the future.
Another good example was Transformers: The Movie, which killed off a lot of characters, in particular Optimus Prime. Sure, it was to sell toys, but that's still pretty gutsy for an 80s cartoon.
The finale of Transformers Animated's second season definitely counts, seeing as it confirmed two long-running fan theories, namely that the Autobots' ship was really a dormant Omega Supreme, and that Sari is at least part robot.
Following up on this, the three part opening movie for the third season was pretty much a wham episode, not giving us much time to recover from the previous episode as it promptly addressed almost every single problem of the finale, and managed to raise even more questions. It was also significantly darker than most of the series had been so far, namely with a more in-depth look at the unethical methods of the High Command and Blurr being murdered by being crushed into a cube onscreen.
After this, the whole series' Wham quotient increases dramatically. The series became noticeably Darker and Edgier and started featuring onscreen character deaths rather than the ambiguous approach used in earlier seasons, along with some rather disturbing material (see: Wasp).
Predacons Rising. "Wasp forgive Bumble-bot... But Waspinator NEVER FORGIVE!"
The episode where Sari learns that she has no birth certificate, social security number, or anything else to prove that she legally exists.
But Cybertron wasn't done yet, oh no. The episode right after had Hot Shot, Scattershot, and Red Alert brought to the brink of death (fortunately, they upgraded in the following episode, but still.) And then there was episode 47, "Guardian", featuring Vector Prime's heart-breaking Heroic Sacrifice. Arguably episode 46, "Showdown", as well.
While we're on the subject of the Unicron Trilogy, Transformers Armada's Cramp certainly qualifies. After half a show's worth of playing in the Heel–Face Revolving Door Starscream goes out to battle with Megatron and lets himself be killed, just to make Megatron form an alliance with the Autobots.
In Transformers Prime, "Partners" has Starscream defecting and becoming neutral, but the true Wham Episode in the series is in "One Shall Rise - Part 1": Earth was formed around Unicron.
"One Shall Rise - Part 3": Unicron is defeated, but Optimus loses his memories of the Autobot-Decepticon war, and leaves with Megatron.
"Crossfire": The Decepticon ranks are reshuffled after Airachnid kills Breakdown (whose remains are recovered by MECH), then goes rogue... along with an army of Insecticons.
"Toxicity": Bulkhead is almost killed and likely permanently damaged. The following episode, "Hurt", has Miko finally lose her innocence after killing Hardshell to save Wheeljack, who becomes alienated from the team for endangering Miko. Not only is Bulkhead stated to never be at the top of his game again, but Hardshell's death finally convinces Megatron of just how dangerous humans really are.]
"Darkest Hour": Optimus destroys the Omega Lock — and any viable chance of restoring Cybertron — in order to prevent Megatron from cyberforming Earth. However, Megatron retaliates by declaring an all out of invasion of Earth, and launching an all out attack on the Autobase. In the ensuing chaos, Wheeljack is shot down by Starscream while the Autobots and humans are scattered as they evacuate the base, which is then blown up by the Nemesis... with Optimus still in it.
"Rebellion": Optimus is revived and rebuilt into a new, far more powerful body using the last of the Forge of Solus Prime's energy, the Autobots led by newcomer Ultra Magnus destroy Darkmount, and the Autobots get a new base.
"Thirst" is probably the biggest wham episode of the third season: Knock Out and Starscream's experiments with Dark and synthetic Energon turn Cylas into a vampiric Terrorcon, whose resulting rampage costs the Decepticons more than half of the Vehicons, and the entire Insecticon horde once Airachnid is freed and banished to one of Cybertron's moons. Cylas is finally killed, and Project Predacon is sped up as well. This leads to a chain of events which ultimately cost the Decepticons victory in the war by the series finale.
The second season finale in ReBoot, which kicked off its first real Story Arc with a bang. The finale was set around an invasion by the web and an Enemy Mine situation. But all within the last few moments it ended up with Bob, who is in every regard the most important person on the show, being betrayed by Megabyte and exiled to the web, leaving the Bratty Half-Pint as the designated hero to stop Megabyte. Compounded by the agony of the third season being stuck for so long in Development Hell.
Used again early in season 3. Remember that new guy keeping Mainframe safe? Well we can kiss him goodbye too.
Sacrifice and a lot of the My Two Bobs arc are pretty whammy themselves.
Frisky Dingo does these quite a lot. The second season plotline of Xander and Killface running for President took a sudden turn when someone finally pointed out that, since Xander's only 32 and Killface isn't a U.S. citizen, neither of them can actually get elected President. In a rage, Killface cripples Xander, kills his cute animal mascot, and vows to finally destroy the world like he said he would in Season 1.
Justice League episode "A Better World" starts off looking like a Batman Cold Open with Superman, Wonder Woman, and Batman fighting their way past Mooks to stop a Big Bad. It's Lex Luthor. No surprise there. But Lex taunts Superman about Supe's complicity in Lex's crimes because Supe always holds the Hero Ball like he's got crazy glue on his palms. Then come the 'whams': (1) Superman murders Lex Luthor; (2) he's glad he did it; (3) the camera pans out the window to reveal that Superman just killed the President of the United States; (4) then the JLA takes over the entire planet! Thank heaven it was an alternate reality. Until they figured out how to come to our world and do the exact same thing.
The 3-part episode ending season 2, "Starcrossed", turns out to be a Wham Episode too. Hawkgirl is The Mole for the Thanagarian Empire, and always has been. She helps them take over the planet. She turns against her own people when she realizes they will destroy her adopted home and helps the Justice League prevail. But the JL satellite is destroyed in the process, and Hawkgirl quits the League before finding out if she had been expelled from the team.
Let's not forget the Justice League Unlimited episodes that dealt with the Cadmus Arc. About half of seasons one and two to be exact.
Culminating in the episode "Question Authority" which had six Wham moments topping each other! Luthor finding out his cancer had gone into remission, The Question finding out the secret of the Justice Lords, The Question deciding to avert fate by killing Luthor so that Superman couldn't, Luthor issuing a Curb-Stomp Battle on the Question and revealing his Presidential campaign was a lie, Superman finding out his old ally Professor Hamilton had volunteered for Cadmus, and Captain Atom showing up at the last moment revealing he has orders to stop Superman from rescuing the Question.
The arc had one more Wham to go; in the last few moments of "Panic In The Sky", we discover that the true Man Behind the Man isn't Luthor, but actually Brainiac, who was fused into Luthor's body.
Dragon Booster's plot changed significantly when Armaggedon showed up in talking amulet form, promising power for Moordryd, the antagonist, which led to him becoming the Shadow Booster and ultimately rebelling against his father. This had far more impact than Mortis revealing that he is Connor, Artha and Lance's dad, and not as dead as they thought. The lack of impact for the latter event was because the fandom had assumed that for months.
King of the Hill has "Death of a Propane Salesman," in which it is revealed that Buckley died in the propane explosion at Mega Lo Mart. Luanne goes slightly insane attempting to hide her grief.
The first season finale of Teen Titans puts the every previous Story Arc episode in a whole new context when Slade reveals that all the villainous plans he set up were just tests of Robin's skill, who he wants to serve as his new apprentice. And is willing to kill all of Robin's friends to make it happen.
"Birthmark" from Season Four has Slade coming back from dead, and revealing that Raven is going to end the world.
Then there's the fourth season finale, where Raven voluntarily brings the world to an end. For a while. Seeing that Slade is a charred skeleton beneath his mask was just gravy.
The Danny Phantom season 1 finale, "Kindred Spirits". For two seasons Vlad has mustered all his energy and strength to make Danny his son. Then we find out in "KS" that he had prepared a back-up plan to complete a perfect clone of him as a substitute (incidentally, that's also why Vlad gave Valerie her first ghost hunting suit) on the off-shot that the real Danny never will come to his side. Shit happens and one Villainous Breakdown later, Vlad changes his mind about the boy; that little bastard is DEAD MEAT.
The season one episode "Public Enemies" also falls under this, as it rather drastically changed the status quo. Before, ghosts were not widely recognized or even known, and so Danny Phantom flew (no pun intended) under the radar. All of a sudden, ghosts become a recognized enemy across the entire city that need to be fought against, and not only that, but Danny Phantom becomes the number one enemy after being framed for kidnapping the mayor! And all orchestrated spectacularly by Walker, whose bastardry will never again be understated.
The Ultimate Enemy. Dear God, The Ultimate Enemy. Danny's life has been going fine until he decides to cheat on the CAT. One small mistake, and everything goes downhill. His friends and family end up dying horribly in an explosion, and with no place to go, he ends up in Wisconsin living with Vlad. The guilt and sadness eats away at the poor kid to the point where he begs Vlad to remove his humanity, allowing him to rid himself of his emotions. Well, that backfires. Horribly. Danny's ghost half rips out Vlad's ghost half and fuses with it, creating a sociopathic monster that destroys most of the earth. The Reset Button got hit, of course, but the whole plot of the episode is just disturbing. And even then, after a season of being Danny's Secret Secret Keeper Danny finally learns that Jazz knows the truth about him. Wham Episode, indeed.
The season 1 finale of Star Wars: The Clone Wars not only introduced an original character, Cad Bane, who immediately comes across as a Badass and unlike most villains thus far succeeds in his mission, nearly wiping out a room full of Senates and an unarmed Skywalker in the process but fueled the launch of Season 2 which in two episodes is already Darker and Edgier than almost everything the first season had to offer.
Also worth noting is various episodes in the series achieved this status by totally reversing the "kiddie" status some of the earlier episodes gave the show. It is likely different for every viewer, but most agree that "Rookies" was the one that paved way for the more mature episodes to come later in the series.
The villains that paved the way for Cad Bane in the Ryloth Trilogy weren't too stupid either, but they each had a fundamental weakness the commander of the blockade did not expect Anakin's suicide run because of his pride, the droid in Innocents of Ryloth did not perceive the Twi'leks themselves as threats until they were ripping him apart, and Emir Tambor stalled long enough for Mace Windu to capture him because of his greed. Unlike these villains Cad Bane's only weakness seems to be that nobody else is as badass as he is.
Season 3's Mortis trilogy, for our two main characters:
Anakin Skywalker realizes the burden on his shoulders as The Chosen One, which was something he previously dismissed as a myth. He also witnesses both himself and Ahsoka turn to the dark side, and will most likely do whatever it takes to stop that from happening. Well, regarding himself turning evil, yeah, about that...
Ahsoka Tano sees a vision of her future self telling her to stay away from Anakin. The Son also tries to convince Ahsoka about something similar, that Anakin wouldn't rescue her when she was held captive. Through "Sithsoka", she also reveals her subconscious fears and resentments: her frustration towards Anakin's criticality and dissatisfaction.
The 4-part Umbara arc in season 4 is one of these (especially since it started right after the Lighter and Softer episodes focused on the Droids), in particular the episode Carnage of Krell.
If that doesn't do the job, at the end of season 4, Darth Maul is back and pissed off, and soon enough becomes one of the villains in season 5. And to show how mad he is, especially at Obi-Wan for slicing him in two, he says he'll slaughter a village unless Obi-Wan comes to him. And : Obi-Wan does come on over, only to find out Darth Maul slaughtered the entire village anyway.. Holy. SHIT.
Even before that, the Nightsisters trilogy in Season 3. Dooku abandoning Ventress pretty much takes the cake, though many other moments qualify.
The Season 5 finale throws one hell of a curveball at us. Ahsoka's name has been cleared, the High Council welcome her back to the Jedi Order, offering to promote her to Knight. We think we're being set up for our little Jedi to take the next step up the ranks... "I'm sorry, Master. I'm not coming back". Ahsoka's faith in the Order has been utterly shattered by them refusing to have faith in her innocence. In response, she leaves the Jedi Order.The end.
Season 1, Episode 10 reveals that Gall Trayvis, one of the few senators to speak out against the Empire, was actually in league with them the entire time. He used his transmissions as a front to hide his true intentions: finding and eliminating insurgents.
Episode 11 sees Grand Moff Tarkin arrive on the scene, only to behead his most incompetent officers, then predict the heroes' next move. While they succeed in hacking the Imperial communciations, Kanan is captured, and Tarkin destroys the tower after only one transmission.
The first season finale is an even BIGGER wham episode. The heroes steal aboard Tarkin's personal Star Destroyer to rescue Kanan. While they get him free, they find the Inquisitor waiting for them. He duels Ezra and Kanan, only to knock Ezra out, causing Kanan to go into an Unstoppable Rage. Kanan then defeats the Inquisitor, driving the latter to suicide. They escape the Star Destroyer, only to have half the Imperial Navy on their tail. But Chopper has gone to get help from another Rebel cell, and rescues them in the nick of time. The episode ends with the reveal that not only did Ahsoka Tano survive Revenge of the Sith, but she has been working for the Rebels the entire time. The final shots of the episode reveal that Palpatine has sent Darth Vader himself to deal with the Rebels. You may wish to take a few minutes to catch your breath after watching the episode.
The Season 2 pilot, The Siege of Lothal, is no less brutal — and follows hot on the heels of the aforementioned finale! Darth Vader sets a trap for the rebels which results in the citizens of Lothal turning against them. They are forced to leave, but find that the Empire has cut off their escape. Sneaking into a nearby Imperial base, they try to steal a shuttle, but find Vader waiting for them. He curbstomps them, and they escape only because he lets them. Then they go to Tarkintown, only to find it burned and its citizens arrested. They finally make their escape back to their fleet — only to find that their shuttle was rigged with a tracking device. Vader shows up moments later, and personally tears their fleet in half, killing nearly all their pilots and destroying their command ship. Only Hera's amazing pilot skills enable them to escape. Even worse, Ahsoka and Vader become aware of each other. Ahsoka is so shaken by the revelation that Ankakin is alive — not to mention that he is a Sith Lord — that she faints, and when she wakes up, she denies any knowledge of who or what he is. Vader, meanwhile, lets the survivors escape again, because he wants to use Ahsoka for his own ends. Oh BABY....
Code Lyoko has one in the Season 2 finale, where Aelita's memory is drained, and XANA escapes the confines of Lyoko. Followed by Franz returning Aelita's memory, which almost totally deletes him.
Then there's the Season 3 finale, which has William becoming The Dragon for XANA.
No mention of Xana forcing William to destroy Lyoko completely by possessing his body through the Scyphozoa? He effortlessly slashes through the Lyoko Warriors with his BFS, then floats off the edge of the highest platform to the Heart of Lyoko. William stabs it, and the entire virtual world collapses in on itself, taking the Sixth Ranger with it.
Season 4's finale was one wham after another. Jeremie's almost finished the program he needs to kill Xana, but the program isn't going down without a fight. When the Warriors are searching for Franz Hopper in the Ice Sector, the AI attacks and possesses William, who was denied the chance to go to Lyoko. What follows (on Earth) is one of the most brutal beatdowns ever seen on the show. The biggest punch: Jeremie's program can't run because it doesn't have enough power. Franz Hopper sacrifices himself to provide that power and dies. And this time, he doesn't come back. Aelita comes out of the scanner crying. She wasn't the only one.
So far, Metalocalypse has three: the season 1 finale, where Dethklok's concert is attacked, the season two finale, where they get attacked again, with the result that their home is burning to the ground and their manager is dying from his injuries, and the season three premiere, where the manager reveals that he had faked his death.
Make that four, with the season 03 finale "Doublebookedklok." Let's count the whams, shall we? Offdensen witnessed Selatcia's Mind Rape of General Crozier in the season 02 finale and may have been affected by it somehow, particularly in relation to Selatcia. The Tribunal are highly suspicious of Offdensen and suspect he has knowledge of their mysterious Falconback Project. And finally, Offdensen is keeping Edgar Jomfru tucked away in Mordhaus and is possibly using him in order to spy on or make plans for the Falconback Project.
Season 4 had three whams IN A ROW! In "Dethdinner", Pickles announces he's quitting the band after getting fed up with Nathan's bullshit. Then, "Breakup Klok" had Mr. Salacia reveal his true form on Dethklok's final concert, and kills their producer Roy Cornickelson. Finally, "Church of the Black Klok" revealed how Ofdensen survived, that Dethklok are part of a prophecy where they are the Chosen Ones, why Nathan destroyed the record (a prophet that guided him) and Cornickelson's funeral is attacked by the Revengencers with Abigail and Toki getting kidnapped (the latter by former Dethklok member Magnus Hammersmith). Holy shit.
In "Dye! Dye! My Darling", the season 4 finale of Daria, tensions between Daria, her best friend Jane and Jane's boyfriend Tom came to a boiling point. The scene where Tom and Daria agree that they can't stab Jane in the back then immediately spontaneously kiss in his car was enough to induce Spit Takes in the audience (a lot of whom declared the series "Ruined FOREVER!" as a result). The episode and thus the season ended with Jane and Tom splitting up, Daria and Jane agreeing they could still be friends but needed to spend some time apart from each other, and with Daria's phone ringing and her answering it to hear "Daria? It's Tom..."
In Iron Man: Armored Adventures, the first season finale is one pretty much from start to finish. Everything that could've gone wrong has done so by the end of it.
Episode 35 of The Secret Saturdays, "And Your Enemies Closer". Argost turns out to be a cryptid himself, the yeti that killed Drew and Doyle's parents, kidnaps Zak, kills Zak's Mirror Universecounterpart by using the Flute of Gilgamesh to steal his Kur powers; which leaves him with the power to raise a army of cryptids. Naturally, the Holy Shit Quotient was through the roof.
Spider-Man: The Animated Series "Turning Point." The Green Goblin learns Spider-Man's true identity and proceeds to wreak havoc on his life. Mary Jane is supposedly killed in the ensuing bridge battle. The viewers know that she survived, but she fell through a time-dilation accelerator portal - leaving her lost in a void and quite a Tear Jerker for poor Peter's reactions.
Followed up down the line by Mary Jane, quite some time after her mysterious return from this, was revealed to have Hydro-Man's powers. As your mouth is still hanging open from that, we find out why - she's a clone made by Miles Warren, and adding the (also a clone) Hydro-Man's power to turn to water and put himself back together helped keep her stable. Unfortunately, it's not perfect, and she does die when her body eventually degenerated, with Peter just as helpless to do anything about it as before.
The Grand Finale of The Spectacular Spider-Man reveals that Norman Osborn was the only Green Goblin, even during season 1 - he'd framed Harry for his crimes and the Norman we saw when "Harry" was elsewhere as the Goblin was in fact the Chameleon. What about the time Harry had the injury the Goblin had sustained? Norman broke his own son's leg. Oh, and you know how in most continuities, Norman is driven nuts or given a Split Personality by his strength enhancers? Well, not so in this one. Harry's overdose made him the perfect patsy, but Norman, using a much more controlled release, was one hundred percent himself, and did all of this with an unaltered mind. Dude.
The two part season finale of Ultimate Spider-Man. After a whole season of dancing around it, Norman Osborn finally becomes the Green Goblin as a result of a fusion of both Spider-Man's blood and the Venom compound. At first driven crazy, he regains his sanity, and seeks to revert his son to Venom. While he fails, a ton of shakeups to the Status Quo happen. Dr. Octopus leaves his services forever, the SHIELD Helicarrier is destroyed (for now), Harry loses the Venom symbiote which Norman takes a sample of, Dr. Connors gets one of his arms crushed, Harry hears of how the Green Goblin came from Spider-man and vows revenge, Spider-Man realizes just how important having a team is, and finally, the rest of the SHIELD team moves in with Peter. Whew.
"The Sinister Six" to a lesser extent. The Sinister Six is created, which test Peter's strength as a leader. In the end, the team does manage to work together and Spidey gets some Character Development. However, the real WHAM is that, although Spider-Man and his team bring in five of the six, Curt Connors fully becomes The Lizard and runs away, leaving Peter feeling helpless after he tried to save him.
In the vein of the "The Sinister Six", "Stan By Me" is another whammer in the Lizard arc. Can be summed up by a sole line by Spidey: "Oh, no. The Lizard part of his brain changed it to drive out Connors? And I just helped! * The Lizard was building a machine that Spidey thought that the Connors part was building in order to drive out the Lizard, so Spidey and company subdue the Lizard and use the machine on him.
"Helga on the Couch" from Hey Arnold!. Helga gets sent to a child psychologist, where the truth comes out about why she acts the way she does...it involves inattentive parents, and a sister whose standards she'd never be able to reach in her parents' eyes.
By the next episode Tom's out of prison and James Woods has been brought back from the dead, but all the other changes so far seem to have stuck, which is also part of the reason why Joyce Kinney was hired as the new TV anchorwoman.
It's not the only Family Guy episode to be a Wham Episode. It's simply titled "Brian and Stewie". The Cold Opening and lack of cutaway gags is a giveaway that something is going to go down. Basically it's about Brian and Stewie locked in a bank vault over a weekend. It had the usual Family Guy antics, including Brian eating Stewie's poop, Stewie drunkenly piercing his ear, and a gun from Brian's safety deposit box ricocheting around the room. It eventually dies down and we're wondering what's about to happen next, then Stewie asks why Brian has a gun. He tells him that it's in case he ever decided to commit suicide as he cannot find a purpose in life, the alcohol meant to be his last drink. Stewie is horrified and admits that Brian is his best friend, and sometimes making another person happy is enough.
"Screams of Silence: The Story of Brenda Q." a Darker and EdgierVery Special Episode that dealt with Domestic Abuse in a straight and serious way. Here, Quagmire tries to help his sister overcome domestic abuse and rub out her abusive boyfriend in a confrontation that takes a turn for the worse.
"The Life of Brian"—- the one where, as you probably have heard by now, Brian dies—-was this when it first aired, since it ended with Brian Griffin still dead and replaced by Vinny...
And then the Christmas Episode a mere three weeks later ended with Stewie preventing Brian's death, and retconing it all off.Seth Green later claimed the whole thing was done for shock value, to remind all the viewers it was a show where anything could happen and likely wood. (Meaning, it was meant to be a Wham Episode with a huge Wham.)
Of all shows from of all studios, Filmation's 1987 cartoon Bravestarr has a Wham Episode dealing with drug abuse, but it refuses to do with it what Cartoon All-Stars to the Rescue did—sugarcoat it. The episode "The Price" deals with a kid who is turned onto a topical controlled substance called Spin. The perps are caught but the tag is tainted: The boy is found in his treehouse, dead of a Spin overdose. The episode ends with the boy's mother in agonized hysteria, with the final "pro-social message" scene showing Bravestarr laying a wreath at the boy's grave.
Before that, "The Fortress of Deception". Other people know about Lance, Ilana, and Octus's secret. Such as government agencies.
Episode 23, "The Devourer", of Monster Allergy has many revelations. Jeremy is placed under Magnacat's mind control after he is caught spying on the meeting between the Gorkas and Dark Phantoms; under his influence, he sabotaged Zick's teleskates that teleports him in Magnacat's hideout instead of Bibbur-Si to warn Timothy of the evil alliance. Zick has lost his powers including his ability to see monsters because his Dom energy is absorbed by the Dom Devourer, but the bright side is Elena, his best friend who can't see monsters, can finally see monsters. Hurray!
The season 2 finale and the season 3 premiere of X-Men: Evolution. For the first two seasons, the show was mostly light, at least when compared to other superhero cartoons. But starting with the end of season 2, the mutants are finally exposed to the world (when before they were hiding themselves) and the show starts going into Darker and Edgier storylines with themes about discrimination, along with the X-Men starting to face larger threats.
Kung Fu Panda 2. Unlike the first film, characters die and are actually confirmed dead, unlike any of the possible "deaths" of the first film. Not only that, the threat they face is greater, and we start to learn about a young Po's tragic past.
In ThunderCats (2011) "Between Brothers." Cheetara and Tygra kiss, Grune is sucked into the Astral Plain, and Panthro loses both arms.
That is nothing compared to "What Lies Above Part 2.'' After all the time we've grown to love Pumyra and her relationship with Lion-O, she turns out to be working for Mumm-Ra. She helps him get the Tech Stone and Avista makes a crash landing. The one good thing to come out of it is all of the Thunder Cats' friends uniting to help in his fight.
The 26th (and final) episode of season 1 of The Avengers: Earth's Mightiest Heroes!, "A Day Unlike Any Other" concludes with the Avengers saving Asgard and, by extension, the world from Loki. However... Captain America has been replaced with a Skrull agent by the end of the episode, setting up next season.
The next season has "Who Can You Trust?" Nick Fury learns that one of the Avengers is really a Skrull. The viewers have known which Avenger the Skrull replaced since the first season endednote see the entry above, so the shock value derives more from seeing the Avengers' dependability give way to paranoia, which even drives three heroes into quitting the team. By the time the episode ends, the Avengers consist of half as many heroes as in the first season, and Captain America takes the leadership position Iron Man renounced. Finally, the viewers learn that the queen of the Skrulls has made her way to Earth, disguised as one of Nick Fury's agents, Mockingbird.
In the first episode of season five, the agents are caught in an attack on ISIS that turns out to be a raid from the FBI, who disband ISIS for never actually being a legally sanctioned spy agency to begin with. Without jobs, the ISIS crew must now find a living in the real world, which they do by attempting, very ineptly, to sell a literal, not figurative, metric tonne of cocaine.
Moral Orel season 2 finale, Nature. Clay takes Orel into a forest for hunting where his behavior suddenly gets tensed of getting drunk, berating him, shooting him in the leg, and refusing to heal his leg. This results in season 3 being changed from light to dark.
El Manana, Gorillaz' music video in which Moe Noodle apparently DIES. Also the Plastic Beach interviews which show Murdoc to now be mentally and physically abusing 2D quite horribly.
The original T.I.E., The Intruder is particularly infamous as this, as it ended the era of the original TOM and saw him replaced by TOM 2.
Its sequel, The Intruder II has managed to outdo it: not only has the Intruder came back, it took over TOM 1's body, assimilate SARA and TOM 4 (albeit the latter offscreen), TOM 5 rips his arm off, and the Absolution is destroyed when TOM 5 triggers a nuclear explosion on the ship the Intruder used to lure the ship there. However, they're also earned their happy ending as TOM managed to back up SARA and upload her onto the new ship and she building him a new arm.
Where's Perry? Part 1 ends with Phineas, Ferb, and their friends falling down a deep gorge, Jeremy apparently breaking up with Candace, Perry, and this is the clincher, suddenly vanishing after being hit by several inators at the same time and Linda and Lawrence without dinner reservations, all of which are thankfully resolved by part 2.
"Happy Birthday, Isabella" manages to breachStatus Quo Is God by having Stacy learn about Perry's identity and avoid getting her mind erased.
"Magical Mystery Cure", in which Twilight rewrites an ancient spell, thereby becoming an alicorn princess. Sweet Celestia, where do we go from here?
"Twilight's Kingdom - Part 2": Let us count the ways: Twilight's library is destroyed; she faces the Big Bad in a battle of Dragon Ball Z proportions; Discord's Heel–Face Turn is nearly complete; the Mane Six are bestowed with new Elements of Harmony in the form of Rainbow Power; Twilight is dubbed Princess of Friendship; and Twilight is given a brand new castle of her very own, with thrones for herself and all her friends (including Spike).
"Crusaders Of The Lost Mark": The Cutie Mark Crusaders finally get their cutie marks, thus ending a major plot arc that had been ongoing since season one. Also, they get their Arch Enemies Diamond Tiara and Silver Spoon to undergo Heel-Face Turns. Unlike Twilight's ascension, which was spoiled weeks beforehand and even during commercial breaks both before and during that episode's first run, there was no warning whatsoever that anything like this was going to happen (aside from some hints in "Appleoosa's Most Wanted", and the fact that it was a Musical Episode like Twilight's and the fifth anniversary of the series, that nobody managed to pick up on). Never before has the fandom been blindsided as it was here.
Robot Chicken: "Fight Club Paradise" begins with the titular chicken escaping from the Mad Scientist's laboratory (thanks to a maid), and ends with him getting revenge on the Mad Scientist after he abducts and tortures his wife whilst killing some characters (and sparing a fair few including The Nerd) in the process, but what really drives the point home is that for once the season ends with the show not getting canceled! Admit it, for a show that gets canceled after every season but gets renewed by the next, this is an exception (Possibly because the bloodbath caused it to get Adored by the Network).
Motorcity: The first episode of the two-part season finale "Vega" is this: Mike asks Julie to lead the burners if "something should happen to him" even though Julie already told Kane she would take over if something were to happen to him, the Duke betrayed the Burners and helped Kane capture Mike, and now Mike is in jail, will be executed and Motorcity is in chaos.
The Batman has the season 1 finale, "The Clayface of Tragedy" with Ethan Bennett being Clayface.
Grojband has the Mid-season finale/Series Fauxnale "Six Strings of Evil"; Mainly for having a Big Dam Plot, it ends with Peaceville getting flooded, and Trina becoming brainwashed by the possessed music box.
TCRI: The Turtle discover the Kraang's headquarters. The Kraang's plan is revealed to be mutating Earth to make it suitable for Kraang habitation, which would kill or mutate everybody else. They summon a giant rock monster from Dimension X that trumps the turtles and has to be taken out by Leatherhead via Heroic Sacrifice - and it still comes back. Finally, the information Donnie retrieved from the headquarters reveals that Kirby O'Neil was just a bystander, and the Kraang's true target was APRIL.
"Showdown": Karai is Miwa Hamato, Splinter's daughter, and she doesn't have a clue.
Annihilation: Earth - Shredder KILLS Splinter and the Earth is destroyed by the Triceratons' black home bomb. Only the Turtles, April, and Casey are alive, rescued by the Fugitoid.
Beware the Batman has episode seven, "Family", where Bruce finds out about Katana's past, fires her and Alfred, is betrayed by Bethanie Ravencroft, and causes a civil war in the League of Assassins between Silver Monkey and Lady Shiva, all of this later revealed to be part of Bruce's master plan to weaken the League and "test" Katana, revealing his identity as Batman to her by the end.
Episode ten, "Sacrifice", had Anarky establishing himself as a major threat by messing with the League of Assassins and using the corpse of Ra's al Ghul as a bargaining chip against them. The episode ends with him returning it to Lady Shiva.
The mid-season finale, "Fall", reveals that Alfred and Tatsu's father had faced Ra's before, and the latter's betrayal might have forced the former to kill him with the Soultaker Sword. Also, Jason Burr overcomes his brainwashing, only to be a victim of the sword, Ra's is revived again, Batman is captured by the League of Assassins, Katana and Alfred barely escape alive, and the League succeeds in using the Ion Cortex to plunge Gotham into darkness.
"Reckoning" brings resolution to the above plot points, but it also has the revelation that Tatsu's father committed suicide by handing over the Soultaker to Alfred so his own soul could be absorbed, leaving Alfred with survivor's guilt. To make up for that, Alfred leaves Bruce and Tatsu to make amends about his past life, which affects Bruce in the long-run. In addition, the commissioner's death leads to Gordon getting promoted and paves the way for Harvey Dent's introduction.
In "Animal", Batman's character arc comes to a head as he becomes too unstable without Alfred and too reckless as his Batman persona, causing him to savagely beat and nearly murder Killer Croc. Alfred returns from his quest to help out Bruce once again.
"Epitaph", within the first minutes, has Bruce Wayne being killed by Batman himself. This starts a chain of events that reveals Dane Lisslow, recurring character and friend of Bruce's, as the fake Batman, Batman's reputation is ruined as he is successfully framed for Lisslow's crimes and is hunted down by the police as a terrorist, Deathstroke is revealed to have survived the events of "Hero", and Harvey Dent is injured and hospitalized. On top of that, Lisslow might not have even existed in the first place.
"Twist" follows up on the events of the previous episode and it lives up to its title as it reveals that Dane Lisslow and Deathstroke are both one of the same, and he has been planning a long, elaborate scheme throughout half of the season to culminate in the destruction of Alfred and Batman. In addition, Anarky "twists" a disfigured and deranged Harvey Dent into getting revenge on those who wronged him, and Gordon quits as commissioner.
The season finale (Which also doubles as the series finale), "Alone" features Katana recruiting all of Batman's previous allies as the "Outsiders" against Deathstroke in a final battle. Deathstroke loses his eye and becomes amnisiac, Batman forms a team, Anarky is ready to continue his dangerous game, and Harvey Dent has new plans for Gotham as Two-Face.
Regular Show with "Steak Me Amadeus". To keep things brief, Margret reveals that she has been accepted into her dream collage and has to move away, leaving both Mordecai and Margret heartbroken.
Clone High has two. The most notable would be the Grand Finale, in which Abe realizes he's in love with Joan, Joan sleeps with JFK, and Scudworth locks them all in a quick freezer with the Secret Board of Shadowy Figures. The second one that might qualify would be "Litter Kills: Literally", which basically revolves around JFK mourning the death of his friend Ponce.
Rick and Morty has "Rick Potion #9" in which Rick and Morty accidentally unleash a Body Horror virus infecting all of Earth and wrecking it beyond repair, then they escape to an alternate universe where they suffered a brutal death very shortly after fixing their version of the problem. They then bury their alternate counterparts, and seamlessly replace them. Morty suffers a huge Heroic BSOD because of this.
"The Wedding Squanchers": It turns out that Rick, Birdperson, Squanchy and other friends of theirs are "terrorists" rebelling against the Galactic Federation. Tammy, Summer's friend and Birdperson's fiancee, turns out to be an undercover agent of the Federation and kills Birdperson, and their wedding turns out to be a sting operation. After Rick forces the family to go on the run with him, the episode ends on a Cliffhanger where Rick turns himself in to the Federation so his family won't suffer because of him and live a normal life on Earth.
"Scarecrow": That new enemy that was literally dug up kills several people, survived that fire, and has taken the face of a spaceport tech to continue his rampage across the galaxy.
"Heart of Tarkon": Wow, Doc really is a Badass after all. Oh, and the Heart of Tarkon is neither a legend or supersition; it's a Benevolent AI that must be awakened to protect the planet. And...its ancient archenemy was The Scarecrow Entity?!
"Armada": Holy Crap! That's a big flotilla of ships headed for Earth! On the upside Their cut-rate starstones led to most of that fleet being destroyed, delivering a devastating blow to the Empire's ability to continue waging war.
The Supertrooper Duology: We knew Senator Wheiner was bad, but we had no idea how bad. And what did he try blackmailing Walsh with? Walsh is Goose's biological father!
The Care Bears & Cousins episode The Bright Stuff finally revealed Wonderheart's belly badge power. A milder example than the other tropes listed here, but keep in mind that in the previous series Care Bears: Welcome to Care-a-Lot, she spends the entire series searching for her power to no avail.