Just before the climax, Rasputin's Morality Pet Bartok opts out, telling him, "You're on your own, sir! This can only end in tears!" He doesn't appear again until the happy ending.
Also, Vladimir is absent during the aforementioned climax in which Anastasia and Dmitri defeat Rasputin.
In Balto, Boris, Muk, Luk and Jenna return to Nome after she's injured saving Balto from the grizzly bear, leaving Balto on his own to help the sled team and recover the medicine for the final third of the film. (Muk and Luk being comic relief characters).
Brave: Merida's three comical brothers stay out of the rescue mission she embarks on to save her mother from King Fergus, and the fight against Mordu immediately after.
In Cars, Mater disappears after Lightning's second night in Radiator Springs. He doesn't return until summoning a stampede of Tractor cows that happens just after the dramatic song "Our Town" that showed the Dark and Troubled Past of Radiator Springs (except for a brief moment in the background).
Cars 3 has several examples. The first of which has Bobby and Cal disappearing after the introduction of the new-gens. Only Cal has a brief appearance afterward. The second is Mack disappearing from the movie before the Florida race that Lightning McQueen competes in. The third example is when Rusty and Dusty are not seen for the rest of the movie after selling Rust-Eze to Sterling, save for a brief appearance in the end credits in which they are seen on vacation.
At the very beginning of Finding Nemo all the fish in the reef disappear when the Barracuda attacks Coral and her eggs and kills them, leaving Nemo as the only survivor and causing Marlin to become overprotective of him. And when Nemo gets taken away by a diver, Mr. Ray and his class immediately swim and hide. And then when Darla arrives, the rest of the Tank Gang besides Gill immediately hide, knowing that she is going to kill Nemo because of her inability to take care of her pets, and don't appear again until after Gill knocks Nemo into a sink drain, causing the dentist to return Gill to his tank.
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 Hey Arnold! The Jungle Movie, Arnold's classmates are left behind in the enemy camp, while Arnold, Gerald and Helga confront La Sombra in the climax.
How to Train Your Dragon (2010): Gobber, Fishlegs, Ruffnut, Tuffnut and Snotlout are notably absent from the scene where Stoick disowns Hiccup, as well as the scene where Hiccup finds that he lost his leg in the battle against the Red Death.
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. Earlier, right before the Art Shift flashback about what really happened to Manny's family, Diego tells Sid to "Shut up" and he stays quiet for the rest of the scene.
Inside Out: Bing Bong, the eccentric imaginary friend who Joy and Sadness spend time with on their journey, actually performs a Heroic Sacrifice to save Joy from disappearing out of existence before the more emotionally heavy climax.
Kung Fu Panda inverts 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 Madagascar, neither the penguins nor the lemurs are present during Marty's confrontation with Alex, who's been driven mad by hunger.
Monster House both plays this trope straight and downplays it. The movie takes on a darker, serious tone when Officers Landers and Lister are eaten by the house. But Chowder, the comic relief of the main trio, is present throughout the rest of the story. Despite this, he's in no mood for jokes, being scared out of his mind. As for the two cops, it's revealed that everyone who was eaten by the house is alive and well and they return to deliver some banter during the credits.
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.
My Little Pony: The Movie (2017): Grubber, Tempest Shadow's gluttonous comic relief sidekick, rarely turns up during the intense climax which pits Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Spike, Pinkie Pie, Fluttershy, Capper and Captain Celaeno against the Storm King's evil forces. Grubber does appear in the ending scene, reformed along with Tempest Shadow.
Zero is largely absent from the climax in which Jack saves Sally and Santa from Oogie Boogie. Zero does show up when Oogie Boogie is nearly killed.
This also applies to Lock, Shock and Barrel who are also absent during Jack's confrontation with Oogie Boogie. They show up after Oogie Boogie is defeated.
The Prince of Egypt: The last time we see the Egyptian priests Hotep and Huy, who are noticeably more "cartoony" than the rest of the cast, Ramses orders them to get out of the palace during the rather intense "Plagues" song.
Rio: Pedro, Nico and Rafael, along several hundred birds escape from the plane before Blu saves Jewel from Nigel. They're later seen in the movie's Dance Party Ending, starting the end credits.
Subverted in Shrek, where Donkey doesn't follow Shrek into the wedding church in the climax, but he does appear on Dragon moments later when she smashes through the window and eats Lord Farquaad whole.
The Ethical Bug is introduced partway through the movie to play off of Jack Horner in his scenes, but he gets flicked away before the third act, and doesn't return until the end to give Jack a coup de grâce.
Played With for Jack himself during the climax. As the most humorous of the film's Big Bad Ensemble, Jack gets trapped in his own Bag of Holding right before Death arrives to claim Puss' life, and he isn't present for the intense duel that follows. Though the conflict seems to be resolved when Death leaves, the now giant-sized Jack suddenly re-emerges as the film's Final Boss, and the ultimate showdown with him is far more comedic in tone than the fight that preceded it.
Smurfs: The Lost Village downplays this trope when Gargamel finds the Smurfs in the third act. The Smurfs all drop their comical personalities when they're frozen with Freezeballs, with Genki Girl Smurfblossom even asking Smurfette, "How could you do this to us?". When Smurfette is turned back into a lump of clay, the trope gets zigzagged as the Smurfs are mourning her, and even Grouchy appears to be in tears over Smurfette's supposed death. It isn't until she comes back to life that the Smurfs' comical personalities come back.
Toy Story 3: When 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, fiery death.
TMNT: Downplayed. The movie focuses more on half the turtles (i.e. Leonardo and Raphael) and the building conflict between them. The other two turtles, Donatello and Michelangelo, only get 20 minutes of screen-time each.
We're Back! A Dinosaur's Story does this with the literal clown Stubbs, as he is seen hiding backstage at the circus when Professor Screweyes shows the feral Rex, Woog, Dweeb and Elsa to the terrified audience, as well as when the feral Rex almost kills Screweyes, only to be stopped by Louie, who returns Rex and the other dinosaurs to normal with Celia's help.
