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Some stories manage a nice balance of silly and serious. But one of the most foreboding aspects of a series about to go a serious route for a Story Arc is the sudden ignoring of 'silly elements', comic relief and other lighter elements of a show. Sometimes they are sent off, leave of their own accord, or are even killed. Occasionally the biggest insult occurs: The writers simply stop talking about the comical elements and focus on the dramatically relevant ones.
Alternatively, the characters may still appear in the story, but without making their usual jokes or humor. In extreme cases, that's the whole idea of the story. In less extreme cases, the characters may receive a "Dude, Not Funny!" rebuke, or simply stay cool because of the ongoing drama.
From an objective writer's standpoint this can seem logical, if you're the sort of writer who feels squicky about needlessly endangering characters. In any case, it can be a big affront to the fans of these elements. Part of a show's attempt to follow the First Law of Tragicomedies. Compare Cerebus Syndrome, This Is Something He's Got to Do Himself. May lead to the show Jumping the Shark if the comedy element was enjoyable or Growing the Beard if the comedy was unfunny. If the characters in question are scrubbed out with no hope of return, it's Kill the Cutie you want.
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Cowboy Bebop's plot sends away its playful kid and cute dog just before the show starts its dramatic swan dive in the final two episodes. Faye also spots the male host of the now-cancelled bounty hunter show out of his hammy character. This also acts as a bit of Character Development for Faye, while being rather sweet as well, as he gets nostalgic about the show.
Digimon Adventure introduced a lot of one-shot comic relief characters early on in the story. Then in the Dark Masters arc, many of them are brought back only to be outright killed to show that things had gotten bad in the Digital World.
In Digimon Xros Wars, Akari and Zenjirou are left behind in the real world while Taiki and Shoutmon return to the Digital World in episode 30.
Defied in One Piece: according to Word of God, he gave Luffy Rubber Man powers specifically so that, no matter how serious things got, at least one "silly" element (the rubber band snapping sound that happens when Luffy uses those powers) would be guaranteed to be in effect at pretty much all times. Ironically, Luffy at a point invents a new fighting technique called Gear 2 which essentially means that he moves so fast that you can't see his limbs stretching. With one of his attacks, Gomu Gomu no Pistol, he stretches his arm extremely long and punches the opponent. In the Gear 2 version of this, he simply holds his hand in front of himself without stretching and then, at an speed invisible to normal eyes (and readers' eyes), he stretches it and punches the opponent. So you don't actually see his arm becoming comically long, you just see the opponent being blasted back. Gear 2 hence is more action-esque and less silly than his usual fighting style, and he uses Gear 2 more often than his old style nowadays. The story balances its tone evenly, with ultra-heavy exceptions in a handful of arcs.
The sudden end of the previously happy, hopeful first episode of Soukou no Strain fits this. Colin, Mary, even Sedi? Their names only lived on to be screamed out by Sara against the injustice of the world.
Sort of a reverse occurred in Sailor Moon. The Outer Senshi, serious characters who represent the pragmatic side of the Sliding Scale of Idealism Versus Cynicism, introduced in the "dark" S season, were completely forgotten in the "goofy" and "childish" SuperS season, only to return when the series again took a darker turn in the Stars season. On the other hand, Chibi-Usa, the star of the SuperS season and one of the main sources of its childishness and goofiness, was Put on a Bus in the Stars season and was not seen again.
Super S: Almost literal, given that the villains of the arc are a circus.
Stars: Aluminum Siren's death signals the end of those silly Phages.
The movies of Mobile Suit Gundam remove the more "Super Robot" elements of the series, such as the G-Armor and some of the goofier enemy mobile armors.
In Tengen Toppa Gurren Lagann, when Kamina dies in a blaze of glory, much of the humor is gone from the series. Kittan takes up most of the humor left, then HE dies in a blaze of glory. Nia takes some humor, but it's more because she can be pretty ditzy. Then SHE dies after marrying Simon (well, not so much "dies" as "is erased from existence"). Violently killing off the recurring cast before the Grand Finale is almost a law for Humongous Mecha series. Tengen Toppa Gurren Lagann, therefore, obeys this with episode 24, although in TTGL style this is done with flair. Jougen and Barinbou, in particular, have their Crowning Moment of Awesome as they make a Heroic Sacrifice to save Gimmy and Darry, then they die laughing maniacally... and take out an Anti-Spiral fleet with their death.
The Cupid Day episode of Code Geass is the last of the show's predominantly-comedic episodes; it ends with Shirley regaining all of her old, traumatic memories, and in the very next episode, Shirley is killed pointlessly, setting both Lelouch and Suzaku on severe revenge paths.
Nightmare of Nunnally and Suzaku of the Counterattack: The Ashford Academy tends to fade around halfway through the series, typically getting only a mere mention at best, and the student council members hardly appear at all.
Busou Renkin. The LXE arc is over, Victor is awake, Kazuki will become like him in six weeks, and a team of Alchemist Warriors lead by Captain Bravo is sent out to kill him before it happens. Time to leave behind Kazuki's school friends for the rest of the series!
In Excel Saga this trope is invoked deliberately, with two episodes that start with the announcement that there will be no gags and things will be a lot more serious. And boy, do they ever. This gets fully compensated though with all kinds of out-of-bounds silliness in the last episode.
Rideback does this in episode 10, when the mostly comedic Suzuri is killed by an act of police brutality.
Kiddy Grade: There is notably less fanservice as the plot becomes far more serious starting at around episode 8.
Index's general condition in A Certain Magical Index is usually a mood indicator. If she's on screen and unharmed, things are probably going to be okay for a while, at least until the scene shifts elsewhere. If she gets hurts or knocked out, however... An example of this is that the series gets serious immediately when Touma returns home at the end of the first episode to find her wounded, when up until then it had been mostly humorous stuff.
Lin's pet dog Pel from the Fist of the North Star anime vanished completely after the Souther story arc, although he was an anime-only character.
Gundam ZZ: The first half of the series was infamous amongst Gundam fans for being incredibly lighthearted and silly, especially when compared to the dark finale of it's previous series Zeta Gundam. However, after a certain point midway through the series, it once again picked up its Tomino style gritty atmosphere. Fun characters Mashymre and Chara are left behind in space, then when they return late in the series, their heads have been messed with.
The Tachikomas, spider tanks with the personalities of cheerful children, get sent back to the lab halfway through the season. (The In-Universe reason is that the humans of Section 9 are worried that the Tachis' emerging self-awareness will negatively impact their performance in battle.) Shortly afterwards, the hunt for the Laughing Man heats up, with several characters nearly dying. Interestingly, the Tachikomas return for the final three episodes, yet this makes the story even more grim: we find out that while they were away, all but three of the Tachikomas died. And the remaining three pull off a very touching Heroic Sacrifice to save Batou. Though being robots whose AIs operate their bodies remotely, the deaths are temporary.
Subverted during the finale of Season 2 when the shit really hits the fan. One of the Tachikoma shyly asks Ichikawa if it could be excused for a while, because it has "something important to do with the other guys". They then hijack the server that holds their AIs and then use it to destroy a nuclear missile before it hits an urban area, killing themselves in the process.
In the beginning of the first episode in Pretear's two-part finale, the show's two biggest comic relief (Yayoi, Himeno's friend at school, and the long-suffering bald butler Tanaka) are shown caught up in a crowd of desperately fleeing townspeople. Tanaka even tries to get back to the family but is unable to do so. Neither are seen again until the happy ending, where all of the Running Gags in the show are given one final hurrah.
In Monster, Otto Heckel — the irreverent small-time crook who spend his days planning to profit off of Tenma's surgical skills in the black market — disappears when the series' focus on child abuse becomes too serious for Plucky Comic Relief.
Most characters from Gintama (especially the main characters) seem to have the default reaction to flee before danger, leaving their comrades behind (often followed by a Taking You with Me moment), all played for the lulz of course. However, when there's a serious arc going on, that behaviour is forgotten and they strive to protect one another in battle.
At the beginning of the Soul Society arc in Bleach (when the Myth Arc kicks in and the human world becomes less important), Ichigo's classmates (besides his True Companions Uryuu, Chad, and Orihime) are sidelined as characters, although they'd been relatively prominent and well-developed during the Substitute Shinigami arc. They remain very minor characters through the rest of the story, occasionally providing comic relief or slice-of-life drama. In the anime, Kon and the Filler mod-souls drop out of sight once the Darker and Edgier Hueco Mundo arc begins.
Gate Keepers recklessly crashed back and forth in between "cheerful" and "dark", finally settling on "dark" for the sequel series.
The Dragon Ball series has been known to switch this trope on and off like a lightswitch. Specifically, most battles from the Red Ribbon Army Saga until the end of series in Dragon Ball and most battles in Dragon Ball Z get very serious, especially after anyone that Goku has befriended or fought alongside has been killed. However, you'll notice that Oolong and Puar end up pretty much becoming background characters... and Lunch, the girl who sneezes and becomes a more violent personality flat out vanishes. Toriyama actually forgot that Lunch existed by the time Z rolled around.
The first few episodes of Naruto were punctuated by several silly Running Gags, including Gender Bending-induced Nose Bleeds and gastrointenstinal malfunction. These stopped getting used very quickly, and haven't shown up in years (save for one guest appearance at the beginning of Part II as a humorous callback to the early days of the series). Fillers, however, have taken those one-off gags from nearly a decade ago and are still running with them whenever some Padding is called for — making for a rather weird inter-franchise example of Never Live It Down.
The final episodes of Angel Beats! feature a battle with shadowy creatures which is preceded by one of the series more comical characters leaves.
In Afro Samurai: Resurrection, Ninja-Ninja gets completely fed up with Afro's insistence that his father has been resurrected, and storms out just before the final battle:
Ninja-Ninja: That's IT! You an IDIOT! And this is far as I go! See ya!
The Katekyo Hitman Reborn! anime uses this trope almost literally, as Lambo (who provides most of the humor) is asleep or unconsious during the more serious battles. The Running Gags also appear more rarely or simply stop appearing when things get serious. One of the more notable examples: the most common running gag was Tsuna's uselessness, which disappears progressively as he takes various levels in badass throughout the series. There is one special subversion right before the final battle. After a whole arc of drama and horrible things, there is a scene where Tsuna's box weapon is bullied by Gokudera's, hilarity ensues. Gamma then lampshades it complaining how it looks more like a school trip than the planning of a war. Reborn replies it is because of that easygoing attitude that they've been able to make it so far.
Sasa from Wandering Son is the ditz of the series, and was one of the recurring main characters. While she still appeared often, she appeared less once the manga hit middle school. The series did however introduce some new, and rather goofy, characters.
While the Penguins from Mawaru-Penguindrum haven't disappeared, their presence is less and less noticed as the series goes into Mind Screw territory.
Starting in the Black and White season of Pokémon, lifetime comedy relief Team Rocket Took a Level in Badass, becoming significantly more competent and foregoing most of the puns and gloating they're known for. They also shift to more espionage and behind the scenes villainy versus ridiculous traps and grand schemes, and even give up on chasing Pikachu, making their run ins with Ash and company purely coincidental. They also got rid of all of their old Pokemon, leaving them behind at the headquarters.
High School Dx D: When Lovable Sex Maniac Issei stops his constant and shameless pervert antics, you know something serious is going down. Then gloriously subverted at the end of Volume 4/Anime Season 2, when Azazel uses his love of breasts to get Issei motivated far better than the villain threatening his friends and family ever did. Vali can't believe it either.
Mid-way through the fourth season of We're Alive the soldiers from Irwin: Puck, Robbins, Muldoon and Carl, mostly known for their back and forth bickering, are attacked by Behemoths inside the jailhouse where Ink was storing them. Robbins, Muldoon and Carl are killed and Puck spends much of the remainder on the series bed-ridden in The Colony's hospital.
The Batman comics have done this several times over the years:
In 1964, Bat-Mite, Ace the Bat-Hound, Batwoman, and the original Bat-Girl were swept under the rug when the "New Look" Batman was launched. The often-silly sci-fi adventures of the previous era also took a back seat to more straightforward detective stories. Believe it or not, the 1966 TV show was actually less silly than most of the Batman stories of the late '50s and early '60s.
After the 1966 Batman show went off the air, there was a considerable and sustained backlash against anything resembling its tone in the comic books. Batman returned to his roots as a "grim avenger of the night" in the '70s. Batman started working alone much more often, with Robin and Batgirl relegated to the sidelines and backup stories.
This trope exists for Batman in-universe as well — it's stated on more than one occasion that Batman gets meaner and angrier when he doesn't have a Robin with him, which is actually how Tim Drake became Robin to begin with (although he originally was trying to convince Dick Grayson to become Robin again).
The story "Urban Renewal" from Batman Black & White: Volume Three has an in-universe occurrence of this trope as its plot. Gotham's particularly bizarre-looking buildings such as a huge globe at the top of a travel bureau, or a building shaped like a giant cash register, are being taken down. One man is waxing nostalgic for these old kitschy locales, and decides to publish a coffee table book dedicated to them—and the one publisher who accepts it is Bruce Wayne, who is himself nostalgic about fighting crime atop these ridiculous buildings back in the day.
Neil Gaiman's story in 1989, Secret Origins Special, features a retired Riddler amidst the same giant novelty objects, musing on the new Darker and Edgier world.
However, very little in comics ever goes completely away. All of the above-mentioned "silly" elements of Batman have been revisited over the years, albeit usually in a "modernized" way.
As with Batman, both Superman and Wonder Woman got the sillies cleared out of their titles in the late sixties and early seventies. In Superman's case, this meant Krypto, Mr. Mxyzptlk, the Bizarro World, Lori the mermaid, the Superman robots, etc., while for Wonder Woman it meant Bird Boy, Merboy, the Glop, the Holiday Girls, even Steve Trevor! In Superman's case, however, the housecleaning didn't "take". Fans really liked Krypto and the Bizarros, so they were brought back after only a few years, and Superman's adventures stayed pretty lighthearted right up until the Crisis on Infinite Earths, after which they became Darker and Edgier. In Wonder Woman's case, though, shooing the clowns kind of crippled the title, because virtually her entire supporting cast had been deemed silly and eliminated (Steve Trevor kept popping in and out, but the rest were just gone). In all the years since, she has never really been able to settle on a single, stable supporting cast or even setting.
This is a good example that "silly" is contextual, too. Mxyzptlk is certainly out-of-place in a more serious tone, but the robot duplicates of Superman, given Kryptonian tech, could have a legitimate place in a more serious story. (As would be proved in 1999's Beware the Superman story Superman Rex.)
One of the three-panel comics of Dirkjan, a Dutch comic, is a literal version of this trope. It goes something like this: Captain Dirkjan to his men: "Men, we're pirates. It's time we get serious. From now on, no more sickbay, you just keep fighting and working. Whoever is too sick to fight is thrown overboard. Any questions?" A clown (who has been offpanel untill now) asks: "What about the clini-clowns?" (= clowns that entertain sick kids in the hospital) Of course it's much funnier in comic-form.
When Judge Dredd started getting darker and more serious in the late '80s, Maria and Walter the Wobot were written out. Walter eventually came back to lead a new robot rebellion, and had to be killed by Dredd.
At around the same time, Strontium Dog started upping the stakes with vicious villains with personal grudges against Johnny and Wulf, and main characters started dying. When this happened, the Gronk just kind of disappeared. He was finally brought back for the Grand Finale of the classic series, but his personality was almost completely inverted.
The Blue Harvest story arc of Star Wars: Dark Times featured H2, a droid with dark humor, whose role in the plot was generally limited to hilarious sarcastic one-liners. As with all Dark Times stories, things continuously got worse and worse for the characters, but when we learned that the beloved Deadpan Snarker got shot and damaged beyond repair, we realized that things went really serious.
Spider-Man stops joking when the Moral Event Horizon gets crossed. In fact, he stops talking at all, leaving you to fight a faceless, voiceless being with spider powers who wants to beat you to death. It's notable that the guy who can joke about anything wasn't laughing when Wolverine made some less-than-appropriate comments about Mary Jane. And then punched Logan through unbreakable glass.
X-Men; during the Mutant Massacre arc in the late '80s, Nightcrawler (a swashbuckling practical joker), Colossus (the Gentle Giant) and Kitty Pryde (The Chick) were Put On The Bus due to injuries sustained against the Marauders. Colossus returned to the team just in time for the Fall Of The Mutants arc, which ended with the world thinking the X-Men were dead, and precipitated one of the teams Darkest and Edgiest periods. Nightcrawler and Kitty went on to co-found Excalibur, the Lighter and Softer X-team at that time.
The core of Flash's comparatively irreverent and small-time Rogues Gallery dies horribly in the first pages of Underworld Unleashed. The Trickster — perhaps the most outwardly ridiculous one of all prior to this — survives and reflects bitterly on the days when he "[rigged] bombs up the butts of rubber chickens. What was I thinking all those years?" He doesn't entirely give up the rubber chickens, though.
After they were introduced into the comic book universe of The Smurfs, the Smurflings are hardly heard from again, mostly appearing as guest stars and cameos, while the stories mainly focus on the adult Smurfs.
In the Astérix story Asterix and Obelix All at Sea, Obelix is turned to stone, and Asterix is openly weeping next to his petrified body. Asterix stories use various standard joke templates, one of which is of three characters who escalate with three increasingly complex puns about the bad situation; and the villagers looking at Obelix all do this with "stone" puns. Asterix cuts them off, telling them to shut up because this is serious and his best friend is dead, and the villagers agree to stop making jokes in poor taste. After this, there aren't any jokes beyond one bit of Laser-Guided Karma at the expense of the Romans who are partially responsible for Obelix's death (they accidentally set their ship on fire when trying to send a signal), one Dark Comedy gag (Getafix thinking the other villagers are smashing Obelix's petrified body to pieces) and one piece of intentionally forced slapstick with Vitalstatistix falling over for no reason. Obelix's prospects of recovery are almost non-existent, Asterix is too busy mourning him to care about his duties as a village warrior, and the Romans are plotting to trap and kill the escaped slaves in the B-plot. The jokes don't start up again until one of the potions they're trying to revive him with finally works, bringing him back (albeit in child form).
Invoked in the MAD parody of Roseanne. When the kids are pondering running away from home, "D.D.T.", whose unintelligible mumbling is almost a guaranteed laugh, starts to speak, but his sister tells him this is no laughing matter.
In Invader ZimDark Fics (and there are a lot of them), this almost always happens to GIR, the cheerful, lovable, childishly innocent robot. To give you a general idea, in one story, Tak, gone crazy with a lust for revenge against Zim, dismantles him and delivers his remains to Zim in a cardboard box.
Kung Fu Pandainverts this for its Final Battle. What looks like the movie's climactic battle, a dark and dangerous duel in the rain that ends with a major Tear Jerker as Tai Lung crosses the Moral Event Horizon... is suddenly interrupted by Po, who appears at the top of the temple steps, doubled over and gasping for air. The sun is shining behind him, signifying that the darkness has passed and now it's time for the real final battle to begin. What follows is one of the greatest examples of how a story's climax can be both hilarious and awesome at the same time.
In Toy Story 3, when the toys are about to be dumped in the garbage truck, Barbie is kept behind by Ken. Later, once they arrive at the landfill, the Little Green Men are apparently killed off by a compactor truck, though they are revealed to be alive and even save the others from certain, firey death.
In Aladdin, the Genie and Iago are pretty much kept to the side as Jafar and Aladdin have their final battle, and Abu and Carpet and taken out of the action by Jafar's magic as well. The Genie is eventually brought into the conflict when Aladdin points out that Jafar is not as powerful as him.
Aladdin: The Return of Jafar is a little better in its treatment of the clowns — in the final confrontation, Abu and the Genie are thrown into peril along with the other heroes, and Iago manages to pull off a Big Damn Heroes. Jafar still manages to take out the Carpet again, though.
The Little Mermaid: During the storm, Sebastian and Flounder are seen dragged beneath the waves and Scuttle the seagull is blown away by the wind, and near the end of the film the first two aforementioned characters are seen cowering in fear at the bottom of the ocean upon watching Ursula's One-Winged Angel transformation, and they are not seen again until the final scene.
The Hunchback of Notre Dame, all of the Gypsies disappear without any explanation when Quasimodo is tied to a torture wheel and splattered with fruit. Esmeralda is seen panicking inside her dressing room, and only comes out to comfort Quasimodo. Later, the gargoyles leave Quasimodo alone when he is mourning the apparent death of Esmeralda and are not seen again until after the battle with Frollo.
The Lion King does this loosely. After the scene in the cave of Pride Rock during the final battle where Pumbaa saves Timon and Zazu from the hyenas, Pumbaa and Timon disappear until Scar is eaten by the hyenas and when they do come back they have no more lines for the rest of the movie. The midquel at least explains what they were doing.
Pocahontas, Mother Willow separates Flit, Meeko and Percy from John Smith and Pocahontas as they share their First Kiss, just before they are attacked by a jealous Kocoum. Later, said characters stay with Grandmother Willow when Pocahontas makes up her mind and goes to confront her father and the settlers. Similarly, Wiggins is seen dressing Ratcliffe into his armor before the song "Savages" and then disappears until after the climax by which point the movie is basically over.
Beauty and the Beast, the servants stay out of the fight between Beast and Gaston, as previously they were seen having their comic battles with the villagers.
The Jungle Book zigzags this, Baloo is knocked unconscious by Shere Khan. The vultures bug Shere Khan which buys Mowgli time to tie the burning branch to his tail.
During the climax of Tangled, Pascal the chameleon runs away and hides when Rapunzel starts to have a conflict with Gothel, and Gothel's murder of Flynn shortly afterward. He eventually comes back to kick Gothel out of the tower just right when Flynn sacrifices himself by cutting off Rapunzel's hair.
Near the end of Dinosaur, Eema, Baylene, Url, Plio, Suri, Yar, and Zini are all forced to stay behind in the Nesting Grounds (which they all entered via a secret passageway they accidentally discovered while they were still trapped in the cave) while Aladar immediately runs back outside to warn the rest of the Herd about Kron's idea for them to scale the ravine, and shortly afterward, the final confrontation with the Carnotaurus.
The Princess and the Frog had a disturbing variation of this: Toward the end of the film, Ray the firefly is crushed to death by Doctor "The Shadow Man" Facilier while trying to smash his talisman in order to turn both Tiana and Naveen back into humans.
Both Terk and Tantor are completely absent during the climax of Tarzan, especially when Tarzan fights Clayton and later, Kerchak's death. No explanation is given.
The two moose are completely absent during the last part of Brother Bear, where Kenai's vengeful brother Denahi has him cornered due to him seeing Kenai as the bear that killed their oldest brother, Sitka. However, the moose start to reappear again when Sitka's ghost comes back to save Kenai by turning him back into a human so that both his brothers can accept their guilt, but do not do anything at all until Kenai decides to remain a bear for the rest of his life.
The floating bubble from The Black Cauldron vanishes during the scene where the Horned King unleashes the dark powers of the Cauldron, and does not return until the three witches use their magic to take back said Cauldron and bring Gurgi back to life. This is also true with Hen-Wen the pig; the film starts to get darker after she runs away from the Horned King's castle.
The Emperor's New Groove first plays this straight when Narrator Kuzco actually stops narrating the film once we see Llama Kuzco stranded in the the middle of the South American jungle (the film's opening shot) once more, but inverts this during the climax.
During the scene in Bambi, when the eponymous character's mother dies, both Thumper the rabbit and Flower the skunk are not present.
In Robin Hood, Little John, the Sheriff, and the villagers do play a part in the jail escape, but they are nowhere to be seen when Robin Hood escapes from Prince John's castle as it burns.
At the end of Sleeping Beauty, the horse is actually scared off after seeing Maleficent as a dragon, and convieniently shows up again after she is defeated.
In The Sword in the Stone, Merlin literalll blows himself to Bermuda in a fit of pique before the jousting tournament. He does come back when Arthur is crowned king, complaining about the modern years.
In Frozen, during the climactic blizzard where Anna rushes to Kristoff, and Hans runs to find and execute Elsa, Olaf is quickly blown away by the storm and Sven ends up stuck on broken ice. On a similar note, the fact that the trolls seem to avert this trope by having a comedic song about love when Kristoff comes to them to seek their help in saving Anna from freezing to death is part of the reason why some people dislike them.
Olaf himself is actually a bit of an inversion. In the first half, Anna and Kristoff were the primary sources of comedy, but as the First Law of Tragicomedies sets in and the characters start to become more serious, Olaf is brought in to keep some lighthearted comedy, due to Olaf not being quite as invested in the drama as they are. (Then again, Olaf's Silly Song winds up being Black Comedy at its finest, further highlighting the darker tonal shift).
In Atlantis The Lost Empire, Mole, Vinny, Dr. Sweet, Audrey, Cookie, and Mrs. Packard all provided humorous moments beforehand. None of them are present during Milo's fight with Rourke.
At the end of A Bug's Life, just before the final battle between the ants and the grasshoppers, Molt (Hopper's cowardly second-in-command and younger brother) actually tears off his exoskeleton and runs off like a coward as the opposing insects begin to fight each other. He doesn't come back until after Hopper is killed by the birds.
In Ice Age, during Manny, Sid and Diego's confrontation against Soto, Scrat is absent. Scrat is not part of their story, so it's pretty much expected.
Monsters University: Around the third act, after the revelation of Sully cheating and Mike's ensuing breakdown and venture into the human world, Oozma Kappa help Sully into the human world and it is then Sully and Mike share a introspective moment alone in the human world while their Oozma Kappa brothers await in the monster world.
Gulliver's Travels has Gabby captured by Bombo's spies in time for the climax, only to be released after Gulliver helps the two kingdoms make peace.
In Madagascar, neither the penguins nor the lemurs are present during Marty's confrontation with Alex, who's been driven mad by hunger. Eventually subverted when the penguins help out during the battle with the fossa.
In The Empire Strikes Back, Luke and R2D2 go to Cloud City to rescue the others. When Luke enters a room to have a dramatic confrontation with Darth Vader, R2 gets locked out. Even earlier than that, Han Solo getting frozen in carbonite, and being taken away to Jabba the Hutt might be an example of this trope, as the film does get more intense and dramatic from then on out.
Jar Jar Binks getting his role greatly reduced throughout the Star Wars prequels is half this trope, half the response to him being The Scrappy.
In Revenge of the Sith Anakin tells R2 to stay with the ship as he makes his way to slaughter the Separatist leaders, later C3PO remains in the ship while Obi-Wan duels with Anakin, only for an off-screen moment for carrying the dying Padme back to the ship. (He does, however, utter one more funny comment just before the movie ends.)
Happens in, of all things, a world war movie, specifically Hitler's SS. When the flamboyant comedian and friend of Rohm, Putzi, gets taken off by the gestapo and winds up beaten to death, you know the Soviet's about to hit the fan. His death not only marks the turning point in the movie, but the turning point in the war, and the scramble by the two brothers to preserve everything they're going to lose no matter who wins the war.
In Fight Club, when Tyler leaves the narrator in the house alone with project mayhem, it marks the turning point in the story when he realizes that things are going too far. Also with Tyler out of the picture, the comedic moments in the film all but dry up.
In the George of the Jungle direct-to-video sequel, Ursula (while not the comic relief of the film) is put to sleep while the big fight at the end happens, regaining consciousness just when it ends. This proves to be odd, as in the previous film, Ursula was actually able to contribute to the ending battle.
In Cirque Du Soleil Journey Of Man, the Flounes who accompany The Everyman literally vanish into thin air after the aerial cube sequence, representing the beginning of the now-adolescent protagonist leaving his youthful ideals behind. They return after he recovers said ideals, when he is The Old Man.
In the 1995 adaptation of A Little Princess, the comical Amelia runs away with the milkman mere seconds before Miss Michin bursts into the attic room, accusing Sara of stealing her locket and seguing into the dramatic climax.
In X-Men: Days of Future Past, every mutant introduced in X-Men: First Class except Havok was killed off at some point between films. First Class is easily the most lighthearted of the X-Men movies and the characters killed—Emma Frost, Angel Salvatore, Banshee, and Azazel—represent its more colorful tone.
In Gravity, crew member Shariff has a funny accent and loves space bungee jumping. He's the first to be removed from the main plotline.
Big Daddy. Nazo. Oh, how funny he is, acting as a composite of the Butt Monkey and the Cloudcuckoolander. Things can never be truly bleak when he's around - can they? We get our answer when Arthur Brooks shows up at Sonny Koufax's apartment and reveals that he has found out about Sonny's defrauding of social services, and that Sonny is now under arrest. Cut to Nazo, who supposedly is too dumb to do anything but make a joke about this - but instead he says to Sonny, sincerely and sympathetically: "I'd like to help you, but my status in this country is not exactly legal." (The character being played by Rob Schneider only makes it all the more cool.)
Although Tim Burton's Batman is pretty dark throughout, it gets darker still toward the end. Comic-relief character Alexander Knox, having just appeared in a slapstick scene, gets legitimately knocked out and doesn't appear again until the finale. Meanwhile, the Joker's bumbling henchmenrun off as the Batplane approaches, the Joker stops being funny for a moment and utters a Precision F-Strike ("Come on, you gruesome son of a bitch - come to me!")...and the Batplane is shot down, crashes, and explodes - apparently killing Batman before girlfriend Vicki Vale's eyes. While frantically trying to clear away the rubble from the crash, Vicki is taken hostage by the Joker and the two go into a church. Batman survives, but he is bleeding and barely able to walk; only his determination to kill the Joker enables him to continue. Once Batman (painfully) reaches the top of the church tower, the "Waltz to the Death" sequence begins and the movie assumes a "lighter", tragicomic tone until the end.
In The Hunchback of Notre Dame the death of Jehan, who had provided nearly all the comic relief in an otherwise serious story, acts as a giant "Bad End Incoming" flag.
Also, initially "funny" characters like Ron and Luna get Character Development which causes them to act more serious as the series winds down. Even Dobby becomes kind of serious before he's killed. Professor Trelawney, however, doesn't become more serious. During the Battle of Hogwarts, she is seen comically hitting Death Eaters with crystal balls, although she's still absent from the final confrontation between Harry and Voldemort (or at least if she's there, it's not mentioned).
In Lloyd Alexander's The High King, the well-meaning but comically inept Prince Rhun is the first character to die, signalling the start of a substantially darker climax to the Chronicles of Prydain.
The mass death of the comic relief Wild Turkeys in The Book of the Dun Cow shows how serious the battle against Cockatrice will be and darkens the mood of the book considerably.
Power Rangers Wild Force: Comic-relief villains Toxica and Jindrax go through a Heel-Face Turn and ride off into the sunset to "find themselves" before the two-part season finale, which is pretty bleak until the last few minutes. Their Hyakujuu Sentai Gaoranger counterparts, by contrast, neither reformed nor survived.
Costume design example: The Fourth Doctor's Iconic Outfit which he wore for most of his run was a brilliantly ridiculous Rummage Sale Reject pile of clothes inspired by then-current Seventies fashion as well as late-Victorian Moulin Rouge bohemians in Perpetual Poverty — most iconically, he wore a ridiculous scarf several times as tall as he was. He tended to flap about in it fabulously, get childish Noodle Implements from the pockets, and it generally reflected how naturally funny his character was as well as his countercultural oddness. When it was decided to make his character more sombre and serious in his final season, he began wearing an elegant, well-coordinated red outfit and a burgundy scarf with a much more subtle pattern that he wore bundled up so it didn't flap everywhere, making him look a lot less funny, as well as more like a Bourgeois Bohemian who was now part of the establishment he instinctively wants to destroy. Naturally, his journey ends in inevitable self-destruction.
"The Deadly Assassin" also begins with a scene where the Doctor decides to leave his scarf behind in the TARDIS, which is just as well since he spends big chunks of the story being tortured and subjected to a No-Holds-Barred Beatdown. It's a nice symbolic indication of how violent the story's going to get, but was probably written in for the sake of the actor's safety.
K9, the funny little Robot Dog, getting blown up early in the Fourth Doctor's season of death-focused stories and just before the "return of the Master" Arc.
The Tenth Doctor's funniest companion was Donna Noble - while she wasn't exclusively Plucky Comic Relief, she and he formed a comic double-act for much of their companionship. Just before the Doctor's death storyline begins, she is dispatched in an extremely unfunny way by the Doctor himself, which, even though he was doing it with the best of intentions, also serves as his Moral Event Horizon. From this point onwards he travels alone and his story is dominated by hubris, Angst and a massive god complex, making him a much less funny and sympathetic character and allowing them to deal sincerely with his slow walk towards death.
Towards the climax of the episode "The End of Time", the Vinvocci — who have mainly been light relief up until this point — leave the Doctor and Wilf on Earth to confront the Master and the Time Lords, after which they decide the Doctor's incoming regeneration is Somebody Else's Problem and fly off in their spaceship to never return.
In Game of Thrones, Plucky Comic Relief and Lovable Coward Hot Pie is shuffled off to a safe place midway through the third season. Following his departure, not only does any hope of a happy ending in Arya's arc (of which he was a part) become extremely unlikely, but the events after he leaves also give little hope of a happy ending for the series as a whole.
In general, the jesters and fools of the novels have either been dropped altogether (Moon Boy, Butterbumps, Patchface) or found their roles severely cut (Ser Dontos Holland)... even the disturbing ones (Shagwell, Jinglebell).
In Teen Wolf, while Stiles is the comedic relief of the show and responsible for a lot of the show's most hilarious moments, his overall role has become significantly less funny as the seasons have progressed. In season 1, he's comic relief. In season 2, he's kidnapped from the lacrosse field and attacked by Gerard Argent. In season 3a, he spends 16 hours dead in a tub of ice water after letting Lydia drown him in order to save his father from becoming a human sacrifice. He spends the first few episodes of 3b basically losing his mind (can't tell when he's awake or dreaming, randomly loses the ability to read), and then comes the reveal that he's possessed by the Big Bad...
For the season two finale of Person of Interest when The Machine is about to go offlineBear disappears. It's explained he was with Leon.
Upon the arrival of the Ghost of Christmas Yet to Come in The Muppet Christmas Carol, Rizzo decides that events have gotten too scary and Gonzo agrees, so they leave with Gonzo turning to the audience and saying, "You're on your own folks, we'll meet you at the finale."
BattleTech does this during the later days of the Fedcom Civil War and all throughout the Jihad. Units and characters whose main purpose was to give a slightly humorous, referential, or colorful flavor to the world are almost all killed off or disbanded, ostensibly to demonstrate that the setting was fully embracing the bleakness of its storyline. This includes units such as the Fighting Uruk-hai, Team Banzai, and Ace Darwin's Whipits among others.
The Fool in King Lear vanishes without explanation before Lear's mad scene and the death-filled Act V, though one theory is that this is merely because The Fool and Cordelia were played by the same actor in Shakespeare's own production. Another theory is that The Fool was killed off offstage: one production opened with a tableau of The Fool and Cordelia hanging side by side on a hangman's noose. A few productions have had him silent but on stage during the mad scene, and Lear killing him during his mania.
In Henry V, Falstaff's offscreen death puts the audience on notice: the former Prince Hal is now King Henry, and can afford no more cheap laughs.
In Hamlet, Rosencrantz and Guildenstern are gotten rid of by the end of Act IV, where Hamlet changes the execution order they're delivering from himself to them. The death of Polonius, meanwhile, sets the act in motion.
The disciples in Godspell are played as literal clowns and wear clown makeup to mark them out as followers of Jesus. He finally calls them together and removes their makeup in the scene immediately preceding his crucifixion and death. Making this more a case of Erase The Clowns.
Lampshaded in Disgaea DS: During New Game+, the Prinny commentary stops during really emotional scenes, usually prefaced with something to the tune of "I'll shut up for awhile." It's back as soon as the dialogue turns goofy again.
Also spoofed in the second to last chapter of Disgaea 2, when Those Two Guys Hanako and Taro (who are, for the most part, just coming along because they're fangirling/fanboying the more plot-important characters) realize that they're going to need real motives if they want to stay relevant (which they, of course, fashion out of complete bullshit on the spot).
When Samurai Shodown III came around, SNK decided they wanted a "darker" atmosphere. This resulted in drastic redesigns for most of the characters (Large Ham Kabuki actor Senryo Kyoshiro apparently Took a Level in Badass), and the removal of the more light-hearted characters, including Gen-an, Cham Cham and her brother Tam Tam, Caffeine Nicotine, Jubei Yagyu (?!) and Charlotte. Samurai Shodown IV came around and added some of them back in, and by Samurai Shodown VI, the entire cast has been reunited.
In Super Mario Galaxy, once you're eligible to enter the final level, you can speak to the Toad Brigade leader, who at first expresses willingness to go to the final confrontation with Bowser, but then gets a headache and says the Toad Brigade can't come after all.
You know that Fire Emblem 7 is about to get dark when Chivalrous Pervert Sain, the closest to a comic relief, shows up less and less in-story (aside of his supports, that is). This could just be explained by how the Fire Emblem series handles storytelling. Since one of the main premises of the series' gameplay is Anyone Can Die, it becomes impossible to have anyone but the main lord(s), enemy characters or NPCs take an active role in the story because those characters may or may not be alive. Which is why latest games (starting with 7, coincidentally) have realized how limiting is this and have around a half-dozen characters or more only "retreat" when defeated and stay on the baselines, injured but alive, so they can talk on plot events.
In Sonic the Hedgehog 2, when playing as Sonic with Tails tagging along (the default play mode), the opening scene of Wing Fortress Zone involves the biplane getting shot down, with Tails inside. Sonic has to tackle this level and Death Egg Zone all by himself. Tails reappears to pull off a Big Damn Heroes moment when it's all through.
Sonic 3 & Knuckles uses this to a lesser extent. Tails follows Sonic all the way through Death Egg Zone, but if you you have all the Chaos Emeralds, then Tails is left behind without any explanation at all after the final boss is defeated and we abruptly cut to The Doomsday Zone, with Super/Hyper Sonic fighting Robotnik's final mecha one-on-one. Justified if you only have the Chaos Emeralds, as Tails can't use them by themselves. If you obtained the Super Emeralds, however... Someone has to make sure that Sonic doesn't land in water. No justification whatsoever if you're playing as Tails solo, though - Robotnik just doesn't manage to run off with the Master Emerald.
In Final Fantasy XIII-2 Mog is "phased out" during a dramatic sequence where Serah is alone in the Void Beyond and has to confront Caius by herself. He's not truly gone, because he's also her weapon and the mechanic for finding hidden treasure, but he may as well be in terms of the storyline.
Several boss fights , including the final one, in Kingdom Hearts II had Sora separated from Donald and Goofy. In the original game, this was played straight at one point (when Sora fights Riku who is possesed by Ansem), but subverted later on in the final battle with Ansem, where Ansem seperates Sora from them but you then have to go rescue your clowns.
In the series as a whole, Donald and Goofy have been doing less and less as more games come out. Lampshaded in Dream Drop Distance, where Goofy asks "Do you think we'll ever get to do something important?" It seems to be turning back around for Kingdom Hearts III.
To show how much more seriousHalo: Reach is than the other games, the Covenant all speak in an indecipherable language, even the formerly Plucky Comic Relief grunts, effectively making them all much scarier. Also a Continuity Nod: the Covenant forces in the very first game only had a few repeating speech sounds, with only 2 or 3 (between ALL the units) being decipherable English.
Tingle, who via GBA link lets players make use of his help in finding extra rupees, fighting enemies with bombs, healing, and finding the Tingle Statues in dungeons, peppered with his silly sense of humor. However, come boss fight time, Tingle quickly excuses himself (with reasons such as embarrassment at meeting Aryll, or a twisted ankle) and Link is left to face the boss alone. Besides the cheapness of being able to Tingle Bomb bosses to death, Tingle would hardly fit in with scenes featuring Link slaying titanic creatures of darkness and reuniting with his sister.
It's the same with Hyrule, where most of the dramatic, plot-relevant things happen. However, the technical reason that the Tingle Tuner doesn't work in these areas is because it only works when the area in question has a map, which neither boss arenas nor the entirety of Hyrule have. Cleverly, it phases pretty damn well into the story justification.
Iji is a very dark game throughout, but many of the logbooks are still quite funny, even if in a Black Comedy way. The humourous logbooks are mostly gone once the Komato arrive, and are gone entirely in the final few levels when things become especially desperate.
In The Legend of Spyro Dawn of the Dragon, before Spyro goes to face Malefor, he tells his adopted brother Sparx that he can't come with him, as he wouldn't survive the journey to the villains' castle. Instead, Spyro asks Sparx to lead everyone underground while the world begins to fall apart. Sparx is shown to be among the survivors after Spyro unleashes his World-Healing Wave.
Pretty much every two-dimensional Super Mario Bros. game starting with Super Mario Bros. 3 does this in its final world. While the final worlds of the first two games plus Super Mario Bros.: The Lost Levels were about as lighthearted as the prior worlds (if considerably more difficult), Mario 3 gave its final world a much Darker and Edgier tone, removing all the toad houses and match games, diminishing the color palette to mostly black and red, and exclusively using the airship, fortress and cave themes for its in-level music. All future two-dimensional Mario games, including the Yoshi's Island games, would do the same kind of thing with their final worlds.
Taiga Fujimura. Whenever she suddenly stops coming over for some reason, things are going to get worse.
Also note that Sakura Matou gets the Unlucky Childhood Friend treatment and disappears around the same time as Taiga in the first two arcs, which is more Shoo Out the Cute than the Clowns. Then comes the Heaven'sFeelscenario.
Arihiko in Tsukihime has a funny tendency to simply stop showing up after about the third day. In Ciel and Akiha's routes he stays slightly more important as they involve the school more.
This happens with a character's mask in DRAMAtical Murder. Clear initially comes across as a pure Cloud Cuckoolander comic relief character who wears a bizarre-looking gas mask all the time. His route starts out as more of the same, with Aoba being continually driven up the wall by his wacky antics. Then Aoba persuades Clear to remove his mask and his route and character do a sudden 180 into What Measure Is a Non-Human? territory and there is literally not a single humorous or light-hearted scene after that.
You can tell a route in Katawa Shoujo is about to get more serious when Hisao's crazy neighbor Kenji stops showing up. In Lilly's route, he shows up after Lilly tells Hisao that she's going to Scotland (albeit while not quite acting like he usually does). Interestingly enough, Shizune's route, he appears in the scene immediately before the bad ending, of all times.
In Super Dangan Ronpa 2, Ibuki Mioda, one lighthearted, cheerful and fairly humorous student, is murdered in the third chapter, as a sign that the game is getting significantly darker.
Any season or mini-series without Donut is going to be much more dramatic than the others.
In episodes focused on the Freelancer project, despite O'Malley, Wyoming, and Gary being prominent villains in the first five seasons, and all having origins lying in the project, their screentime has been greatly limited, with only Wyoming getting a few brief lines. This is due to how their goofier personalities would clash with the more serious tone of the Freelancer segments.
O'Malley/Omega got a minor form of this in the opening of Reconstruction. In Blood Gulch Chronicles, he manifested as a parody Omnicidal ManiacSplit Personality of whoever he was infecting. In the opening of season six, we hear the account of a shell-shocked soldier who had dealt with O'Malley arriving in his vicinity... and it's not played for laughs.
It's implied this is because O'Malley had only infected idiots, resistant pacifists, or Texas before. Once in some semi-competent soldiers with some actual aggression to use...
El Goonish Shive has, for example, phased out the "anime martial arts instructor" (a character who exists almost solely for comedy, e.g. trying to go "super saiyan" in his first appearance), in favor of Nanase's mother (a character who exists solely to cause drama, e.g. criticizing Nanase for not spending every single waking hour devoted to schoolwork and then punishing her for objecting to this).
The "Fire and Rain" Story Arc (a large peak in seriousness in the first five years of the comic) occurred in Nebraska, thousands of miles away from the usual setting, with no Talking Animals, Mad Scientists, or any of the strip's other wacky attributes. Just an insane assassin and a terrified coed. Okay, one person gets turned into a camel, but even that was treated pretty seriously by the comic's standards.
Years later, Kiki is similarly absent for the entirety of the "bROKEN" Story Arc. She appears sleeping in the background at some point and then isn't seen until after the funerals.
Early in Dresden Codak's "Hob" Arc, Tiny Carl Jung is invited by the Tokamak's to accompany them in seeing Kimiko's newest discovery. He declines.
The author has pointed out that some of the trolls receive more focus in the comic due to being more important to the plot, with the less important ones generally staying in the background. With the storyline becoming more serious and the stakes becoming higher, it seems somewhat telling that among these Demoted to Extra trolls are Nepeta and Gamzee, while Vriska not only is counted as an important character, but the one responsible for setting the events of the entire arc in motion. Gamzee has since come roaring back into the plot, or at least the trolls' segment of it, but surprise surprise: he's shed the comic relief mantle. Though he's still hilarious in a dark sort of way.
Earlier, Jade's dreambot was a silly little source of Plucky Comic Relief and general cuteness. At the end of act four, however, it malfunctions and explodes after Jade's dreamself dies, marking the beginning of Homestuck becoming a much more serious story.
Bricky (a talking brick) will often disappear from The Life of Nob T. Mouse when a more serious storyline is running. The exception was when Knight of Cerebus Grandfather Time first arrived however, as Bricky played a key role in defeating the Grandfather's minions.
Tom Siddell typically has some humorous blurb under the strips of Gunnerkrigg Court. He always shuts up when the plot dips into genuinely somber material, especially if it involves backstory concerning Annie's late mother.
Tom: Page notes will return when the chapter stops being about dead people. Come on.
Throughout the darkest Penny and Aggie arc, "Missing Person," involving the investigation of a kidnapping and climaxing in attempted murder turned attempted suicide, CloudcuckoolanderGenki Girl Lisa Winklemeyer is absent with the exception of a silent and understated two-panel appearance early on.
Survival of the Fittest, once the game is more than half-finished. At the start, there seem to be some comic relief characters, and some other stuff that seems a bit odd and out of place in such a grim situation, mostly Narmish or just good humoured. This is fixed by the second half. Once the characters remaining are dawned upon with the fact that they are the only ones left alive out of 200+ classmates, even more noticable towards the end, the comedy evaporates, and the shit does down.
In Atop the Fourth Wall, Linkara's Conflict with "The Entity" is preceded by its slowly absorbing everyone else on earth, thus eliminating the quirky, humorous supporting characters (Ninja-Style Dancer, Harvey Finevoice, Pollo, Iron Liz) and leaving Linkara to face it alone. Interestingly, the biggest "clown" in the cast, 90s Kid, is instead possessed by the entity, so he is still at least physically present (as much as he usually is anyway; Linkara plays him), but behaving in a far from humorous manner.
Avatar: The Last Airbender has a recurring non-permanent version, as the presence of Momo is often a mood indicator, and he has a tendency to disappear when things are getting serious.
Averted in "Lake Laogai", when at the start of a battle Momo flies off... only to return a few seconds later with Appa.
Lampshaded in the Grand Finale: before Aang fights Ozai, he says, "Momo, time for you to go." Momo coming back is a sign that it's all over.
In the Momo segment of "Tales of Ba Sing Se", his story has some quite serious bits (though also still has its fair share of goofy). It's also the only story with any relevance to the story arc, as it ends with him discovering a place where the missing Appa was held.
Pro Bending announcer Shiro Shinobi's comical reporting style made it through the entire Equalist invasion of the stadium until violently being cut off to make way for Amon's arrival.
Though it averts it with Korra's polar bear dog Naga, and Mako and Bolin's pet fire ferret Pabu the equivalents of Appa and Momo in the original series though Bolin tells them to stay put away from the fighting in the two part finale of season 1 Naga and Pabu turn out to be pretty important when they ignore his instruction and come to save him and Asami from capture, and Naga is a pretty good fighter.
Earlier than that, when the Equalists attack the pro-bending arena, Pabu chews through the ropes binding Bolin, Korra, and Mako, freeing them to fight.
In Justice League, The Flash is notably absent in several serious scenes such as in the league's first confrontation with Darkseid.
Though the series itself, much like examples mentioned under the Batman entry, averts this. The whole idea of the "Justice Lords" universe is that the League itself gets too dark when the clown isn't around, to the detriment of the entire world.
Also subverted a lot in Unlimited. A lot of the Flash's time is spent showing how great of a hero he is in spite of his clownish nature, and sometimes, even because of it.
This also happens on and off with the humans in Transformers Prime, and by and large the humans are back shortly afterwards. So far, they've been absent from the episodes "Partners", "Loose Cannons" with the exception of Agent Fowler (who was in serious overdrive), and "Crossfire".
Starting in season 2, the children appear very sparingly, and end up in more danger when they do appear. In the season two finale, they have one appearance to lampshade their lack of appearances of late. And then they get kidnapped and held hostage.
Done in Wakfu for the climactic three final episodes of season 1. Grufon the Map Shushu is unaccounted for after episode 18. Az the Tofu is entrusted to Canar's care in episode 24 before Yugo join back his friends for the finale battle. The same could be argued for Sadlygrove's death in episode 25, though things were already quite serious by then. Possibly the case for Ruel as well, considering that he was separated from and hardly even mentioned by the other heroes for several episodes, only to have a bit part in the finale.
When ReBoot went Darker and Edgier, Megabyte didn't just shoo the goofy Hack & Slash. He tried to kill them by sending the two to the front lines and certain destruction.
Done in a way in Total Drama World Tour. Every single elimination in the first half of the season, barring Izzy, was from Team Victory, lighthearted and easygoing characters. Once they were gone, all that remained to get rid of was Noah. With every funny character gone (except Owen and Tyler), that made room for drama with the love triangle that took up about three episodes. Things lightened up a little after Gwen, Courtney, and Duncan were voted off though.
In the episode "Plankton's Army", SpongeBob is absent from the scene where Plankton has Mr. Krabs and Squidward trapped in the toilet. He reappears after Plankton and his bretheren find out about the Krabby Patty formula. This is an odd case, as the preceedings that go on without him are just as clownish.
SpongeBob is mostly absent during "One Coarse Meal", which is considered one of the darkest episodes of the series.
In the Phineas and Ferb episode "Phineas and Ferb Get Busted", both Perry the Platypus and Dr. Doofenschmirtz are completely absent... until they show up at the climax for a Deus ex Machina, where Perry shows up fighting Doof while at the same time saving the boys and Candace from the Sergeant.
This is done to Sgt Blob's team in pilot episode of The Dreamstone, who are defeated and dissappear from the conflict shortly before Pildit's Disney Death and Rufus' showdown with Zordrak, not appearing until the conflict is over (though other similarly clownish Urpneys appear during the climax). This is something of Early Installment Weirdness, since the Urpneys would act as Villain Protagonists for the rest of the series onwards (though it is repeated in a couple of rare instances Zordrak once again takes part in a scheme).