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At the climax of All Dogs Go to Heaven 2, Red assumes his gigantic true form after capturing all the dogs in Heaven with Gabriel's Horn. Truthfully, it's just an incredibly massive and more demonic version of his base form, but is still enough to prove a major problem... until Charlie discovers his weakness.
The Queen's "perfect disguise" in Snow White certainly counts, depending whom you ask; it's absolutely terrifying enough and—more importantly—it reflects the Queen's true nature. Supremely ironic given that the Queen wants to be "Fairest of Them All".
In Sleeping Beauty Maleficent turns into a dragon to fight Prince Philip, respectively.
Maleficent: Now shall you deal with me, O Prince, and all the powers of Hell!
In The Little Mermaid, when Ariel doesn't get Eric's kiss within the time limit, Ursula allows King Triton to trade himself for his youngest, and she takes his trident and uses it to turn into a giant version of herself. Then Eric crashes his ship into her, impaling her and also electrocuting her, oddly.
This seems brilliant only in the context of the rules set by the film; Aladdin used a Chekhov's Gun of a comment of the genie's back at the oasis. The actual djinni even in the proper translated Thousand And One Nights are enslaved in precisely one story: Aladdin, which features a 'slave of the ring' and a 'slave of the lamp.'
There was a mysterious slave from nowhere that dumped the transformed fish in the fire in 'The Fisherman and the Genie.' He may have been a genie himself, although the title character was just shut up in a jug so long he resolved to kill whoever let him out.
Played with in Aladdin: The Return of Jafar in that it's actually his original, real form at the start of the film, but Jafar decides to transition back into his gigantic Genie self for the final battle instead of the human he looked like for most of it. Unlike the first film, it's not in any way a Clipped Wing Angel.
"You're crazy!" "No. Spiteful, vindictive, VERY large but never crazy."
Parodied in The Emperors New Groove: Yzma is exposed to one of her own potions, and emerges laughing maniacally from a huge cloud of smoke only to be revealed as... a cute little kitten.
In an even more comical version, Kronk's New Groove features Yzma using a potion that will turn her into something that her enemies (in this case a bunch of old people who she sold fake potions to) cannot harm... a cute little bunny. Unfortunately for her, while they don't harm her, the local condor doesn't mind taking her for food.
In one episode of The Emperor's New School Yzma does turn into a giant snake. And in another episode she and Kuzco have a transformation potion duel—one of the things Yzma turns into is a Tyranosaurus Rex.
And she once made a potion that would turn her into the most hideous, terrifying thing imaginable, so frightening the other wouldn't be able to do anything about her... comically subverted when the potion does nothing, implying that she already is.
In the video game for the film, Yzma actually attempts to do this on the last level of the game by drinking a potion... and, true to the film, ends up becoming a cute little kitten. She and Kuzco then race each other for the human potion.
Yzma: *holding a potion* Ahhh, Kuzco, I'm glad you made it. Now, with this potion, I will turn myself into a hideous monster, and END YOUR RULE FOREVER!!!!
Kuzco: Are you sure you didn't drink it already, you old bag of bones?
In Wreck-It Ralph, King Candy/Turbo is eaten by a Cy-Bug. He takes it over and becomes a massive fusion of himself and the Cy-Bug.
Downplayed in Frozen with Elsa's snow creature "Marshmallow" (as named by Olaf). Already intimidating to begin with, making him angry causes him to sprout giant ice spikes and send him on a rampage.
Appropriately for a film that (ahem) was an intentional homage to the classic films, Rothbart in The Swan Princess has the ability to become "The Great Animal". His monstrous true form was teased throughout the entire movie until the very end - only to have him bring the Narm and change into what appears to be a big fruitbat.
Don Bluth likes Disney movies as well and has used this at least twice:
In the already insane Rock-A-Doodle, the Grand Duke appears to puke his evil magic up all over himself and mutates into a sort of gigantic owlish... tornado-ish... thing...
The spin-off movie Bartok the Magnificent has Ludmilla (voiced by Catherine O'Hara of SCTV) steal a potion that Babayaga has given Bartok to aid him in his quest - it turns you into whatever you are, deep down inside. She drinks it and...
Don Bluth actually worked for Disney around the time of movies like The Rescuers, so he was just carrying on the tradition.
Hexxus in FernGully: The Last Rainforest. After Hexxus' power source from human pollution is disconnected his smoke form dissipitates, and it momentarily seems like he's defeated. Then he harnasses his own power and transforms into a giant, black, cloaked skeleton made out of fire and tar. It's hinted to be his real form, as it's glimpsed earlier in the film during his Villain Song.
Simone Lenoir, Lena Dupree, and Jacques undergo this trope in the finale of Scooby-Doo on Zombie Island when they transform into hideous, mindlessly snarling, spiritual life energy draining vampires that look like were-versions of cats. It is implied that this is their true form after they made a deal with the statue of an eldritch Cat God that is supposedly an evil version of Bast.
The Teenage Mutant Ninja Turtles cartoon that only aired in Japan (and has gained a bit of notoriety online as many viewers assume that it must be an elaborate parody). In this series, the Turtles were granted magical crystals that allowed them to transform into superpowered forms. Sadly, Shredder, Rocksteady, and Beebop found evil versions of the same crystals and are now capable of turning into superpowered monsters. At this point, it's probably better just to direct your attention to the show's opening sequence.
Happens all the damn time in Men In Black (both the comic, movies, and AnimatedAdaptation) whenever the disguised alien villains expose themselves in front of J and/or K. One has to wonder why they don't just shoot before the transformation is complete, what with the guns usually loaded and pointed at the alien during the transformation.
However, they may be following the grand tradition of movie aliens flipping out and assuming monstrous forms to attack. The Thing (1982) does it (quite a lot really). So does Sil in Species.
For the first film, it was justified since the Bug had eaten the galaxy and shooting him would probably have destroyed it. Subverted in the third film - after Boris kills J's father, he starts transforming and sneers "Go ahead, arrest me," at young-K. K calmly replies "Not today" and disintegrates him with one shot.
Happens to the villains in both 2003's Hulk and 2008's The Incredible Hulk. Then again, this makes sense as The Hulk himself could qualify as the heroic version.
An early idea for The Lord of the Rings grand finale was to show Aragorn battling Sauron in the last battle. Sauron (just an gigantic red eye up to this point) would first be seen as a tempting angelic bishonen◊ (Kate Winslet in cameo) who then transform into the gigantic armored fighter seen in the first movie's prologue. The filmmakers eventually decided that this was silly (and an inconsistency, since they had decided that Sauron wasn't supposed to be powerful and capable of fighting without his ring) and replaced the armored Sauron with a troll.
This is because Sauron is a Maia (angel), sort of like Gandalf. The beautiful side was his original form and he used it to corrupt Aragorn's ancestors. Eru Ilúvatar destroyed Númenor and Sauron lost his body. He recovered, but could never regain his beautiful form and had come up with a badass one instead. Thus the above scenario would have violated canon, but that probably wouldn't have bothered the film makers since they had already swapped Sauron's physical book-form for a giant red eyeball.
Dracula and his brides in Van Helsing can turn into harpy-esque bat things. And in the finale, Van Helsing himself becomes a werewolf to battle Dracula, who has turned into a giant demon thing.
According to the bonus features on the DVD of the first Blade movie, this was the original ending of the film, with villain Deacon Frost transforming into the blood god La Magra (who looked like a giant CGI red tornado). However, the filmmakers were struck with a jolt of good sense and realized that it would detract from the climax, having just spent the entire film building up Frost as the main villain. Instead, La Magra possesses Frost, granting him nigh-invincibility and fighting prowess.
The Penguin in Batman Returns is another non-fantastic example. As a derelict living in the sewers, he wears nothing but a thick robe over slime-stained long underwear. Once he decides to compete in Gotham City's mayoral race, he begins appearing in public in a tuxedo shirt, a waistcoat, striped pants, a bow tie, and a top hat. Fleeing the city in disgrace after his hypocrisy is exposed by Batman, Penguin loses his hat and retreats back into the sewers, where he begins stripping off his fancy suit. For the rest of the movie, he appears only in his robe-and-long-underwear combo - signaling that he has returned to his "normal," quasi-animalistic self.
Although it's debatable if the Hessian counts as a villain...the Hessian Horseman's head growing back at the end of Sleepy Hollow' could also qualify.
Some of the monsters in the Godzilla series can change form. For example, in Godzilla Final Wars, Monster X transforms from a skeletal dragon into the more powerful Keizer Ghidorah (Which is essentially an Expy of both King Ghidorah and Desghidorah (a quadrupedal three-headed dragon Kaiju)).
Likewise, there's Destoroyah who changes from a pretty dang big crab/scorpion-esque monster into what looks like a kaiju version of The Devil that towers over Godzilla himself.
In Lisztomania, Richard Wagner turns into a grotesque vampire at the final showdown with Franz Liszt.
Ghostbusters has the scene at the beginning where the librarian ghost turns into a hideous ghoul when the GBs are trying to get her. Interestingly enough, there was an earlier librarian ghost puppet that got rejected because it was too scary, but it was recycled and used in the 1985 vampire film Fright Night (see below).
Parodied at the end when Gozer, who initially appeared as a young woman, demands the Ghostbusters choose the form it will use to destroy them. All the GBs clear their minds except Ray - who unintentionally thinks of the Stay-Puft Marshmallow Man. Cue the attack of a 50-foot mascot.
And technically, this also happens to Zuul and Vinz Clortho, where, after they complete the mating ritual and get zapped by Gozer's lightning, they burst out of their human disguises and resume their natural Terror Dog forms, only to not do anything more for the rest of the film until they are ultimately destroyed and turned back into stone statues by the destruction of the gateway to Gozer's dimension.
The Witches of Eastwick has the scene where Jack Nicholson's character becomes a giant and then after the girls smash the wax voodoo doll of him becomes a worm-like monster.
In the 1985 vampire film Fright Night the vampires have three phases of transformation, the first is typically like a normal human, the second is like a normal human but with fangs, and the third phase is a extremely crazy looking monstrous creature with More Teeth than the Osmond Family. At the end Jerry Dandridge (the main vampire) turns into a human/bat hybrid thing, gets hit by sunlight and bursts into flames and finally dies. Interestingly enough, the vampiric version of Amy is in fact a recycled version of the rejected librarian ghost from Ghostbusters.
The main villain in the 1980s Eddie Murphy Vehicle The Golden Child spends most of the film looking like actor Charles Dance. At the Final Battle, and with no foreshadowing anywhere in the film, he transforms into a large, bony, winged demon (stop-motion animated to boot), whereupon Murphy kills him with a special knife.
Eddie Quist's transformation into a werewolf near the end of The Howling could be called this.
Toward the end of Conan the Barbarian (1982) (1982), the villain Thulsa Doom (played by James Earl Jones) turns into a snake to emphasize his inhumanity, though Conan doesn't actually fight him in that form.
At the end of the stop motion film, Jack the Giant Killer, after several attempts to kill Jack (the main character) are foiled, Pendragon, the main villain and evil sorcerer, transforms into a dragon to fight Jack, who eventually kills him in the final battle.
In Return to Oz, once Dorothy begins guessing right at the ornaments and restoring the Scarecrow, Tik Tok, and Jack to their original forms, the Nome King, previously human-sized and at one point almost looking entirely human, becomes a giant rock monster and attempts to eat them all. Unfortunately for him, Billina was inside Jack's head, and laid an egg, which fell into his mouth... POISON... TO... NOMES!!!
At the end of the first Guyvermovie, Fulton Balcus, the head Zoanoid, turns into a giant creature after the main character refuses his invitation to join Chronos. The transformation is shown in the dark. All you can see are his Glowing Eyes of Doom, as they raise and separate to show just how big he has become. To his credit, taking him down requires the Guyver to use his secret weapon - a Wave Motion Gun in his chest.
In the sequel Guyver 2: Dark Hero, Crane, a reptile zoanoid and main antagonist, gets his own (though damaged) guyver unit and turns into bad-ass incarnate.
During the final battle of Mega Monster Battle: Ultra Galaxy Legends, Ultraman Zero manages to defeat Ultraman Belial by throwing him into a pit of lava. He's soon followed by the souls of his 100 kaiju, merging with them to form the 100 Union Kaiju Beryudora. It takes an all out attack from the Ultras, EX Gomora, and Ultraman Zero to finally put him down. And Belial still survived!
In the first Hellboy film, every time Rasputin dies, a little bit more of his god comes with him, until at the end of the film, he dies one last time, his body splits open, and a full-fledged Eldritch Abomination emerges.
In the climax of Hop, holding the egg of destiny transforms Carlos into a giant, freakish bunny/chick amalgamation.
Eddie Valiant: Holy smoke, he's a Toon! Doom: Surprised? Eddie: Not really. That lame-brain freeway idea could only be cooked up by a Toon. Doom: Not just ANY Toon... (reveals his true identity) Remember me, Eddie?! When I killed your brother, I talked! JUST! LIKE!!THIIIIISSS!!!!!
In Man of Steel, Zod starts out like his fellow soldiers jumping around at high heights and having Super Strength and speed. But when he breaks out of his battle suit during the final battle, he becomes as equally powerful as Superman, with the ability to fly and use heat vision.
In Wishmaster, the Djinn adopts his true djinn form whenever things get serious. He also appears like this when he gets defeated in the climax of every one of the movies, demonstrating that it's a true monster being overcome by the protagonists.
Djinn: Spare me, child. Behold my true face.
Alexandra: Oh my god.
Djinn:Yesss. The shit just "hit the fan", didn't it?
The true form of the renegade spirits in R.I.P.D..
An almost literal example in End of Days. After Satan's human host is damaged beyond repair he abandons it and manifests in his true form as a gigantic, winged demon/dragon before possessing the hero.