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In Simoun everyone is born female and upon turning seventeen go to a mystical spring where they choose to either remain female or become male. For those who choose to become male the process is a Slow Transformation. For example head mechanic Wapōrif went to the spring and became male two years before the series but still has the biggest bust in the series.
The werewolves of the Ginger Snaps films transform slowly into wolflike creatures, over the course of days or weeks.
Seth's horrific transformation in The Fly (1986) starts out gradually with his fingernails becoming loose and his face having a subtle discoloration to it. Then his body parts begin falling off, starting with his ears, and the Body Horror climaxes with his decaying human skin being torn apart to reveal his true mutant fly form.
Wikus's transformation into a Prawn in District 9, to the point where by the very end, he's become one entirely.
In Lost in Space Dr Smith receives a spider bite — two decades later he's transformed into a huge spider creature.
When Tash is infected in Galaxy of Fear she starts off with a rash that, through that story, swells and spreads, sends off Tainted Veins, and she sweats and is unusually irritable. Then the rash starts oozing... then the ooze proves to be tendrils of the Blob Monster that she's turning into and moving about as the transformation speeds up. This is in a day or so.
Stock in trade of the Evilutionary Biologists in The Moreau Factor. Somewhat mitigated by the fact that their victims are mostly other scientists deliberately chosen because they would find the research opportunities presented by their transformations (if not the actual transformations themselves) intriguing.
In Seraphina Dragonís muscles are soft, and their wings incapable of flight for the first few minutes after transformation.
In Lord of the Rings, Gollum's transformation from hobbit to.... thing was centuries-long. It is implied that the Nazgul's transformation from humans to dark holes in reality was one, too.
There is an episode of The Outer Limits where a person is getting weird warts and such. It turns out that a race of reptiloid aliens had sent spies to study humans and the spies are turning back after the disguise wears off. The horror factor is the spies themselves didn't know they were aliens.
The Round the Twist episode "Nails" starts with a distressed boy showing the protagonist he now has three rows of nails, and telling her he's turning into a monster. By the end of the episode, he has become a merman.
In BIONICLE, after the Piraka bathe in mutagenic water for a short while, thanks to falling into a trap, they don't notice it, but they start developing aquatic capabilities. When we next meet them a couple of books later, we find that their whole bodies have diminished, reducing them to eel-like spines with their heads at the end.
In Guild Wars Nightfall, Varesh transforms into a Margonite like appearence (and eventually a full margonite form) over the course of several missions. This involves getting 2 extra pairs of eyes (first appearing as bumbs, then fully appearing) and become a lot paler.
The Wanderer over several cutscenes in Diablo 2 gradually looks more and more evil, until in a final cutscene morphing fully into a Diablo form.
In Eternal Darkness one of the characters you play as is inflicted with a curse in their chapter, meaning he gradually rots and turns into an undead creature (this happens at set points in the level) while he tries to to warn Charlemagne before he meets the same fate. He fails and ends up trapped in a room in the church as an undead monster until another character finally puts him out of his misery in a boss battle a few hundred years later.
The most notable thing about the online retro dungeon-crawling RPG The Haunted Ruins is how the general shopkeeper slowly transforms from a seemingly innocent girl into an evil witch the deeper you venture into the dungeon. At first it looks like she just put on makeup, but then her ears become pointy, her cashier uniform becomes a skimpy dress, and a tiara and pointy nose begin to gradually form on her. This transformation is mostly amusing to watch because of how she keeps on insisting that her changing appearance is all in your head and how you simply MUST show the fabled "Dark Orb" to her as soon as you find it, mmkay?
The protagonist of Shadow of the Colossus gradually becomes battle-worn as he kills the Colossi. There is, eventually, an explanation for this.
In Skullgirls, this happens to Filia during her ending: Upon finding the Skull Heart, she wishes for Painwheel to return to normal, a seemingly pure wish that should be granted without problem by the Skull Heart note If the Skull Heart decides your wish is impure, you become the next Skullgirl. However, the Skull Heart finds that her motivations are not entirely selfless: Filia's wish is partially motivated by her desire to atone for her actions during her life as a member of Medici family. As a result, poor Filia is next in line for the title of Skullgirl, but since the wish was not entirely selfish, the transformation is not instant, allowing her to at least enjoy life with her childhood friend for a while.
A similar thing happens in Parasoul's ending. In order to save her sister, Umbrella, from becoming the next Skullgirl, she wishes that Umbrella will never become the Skullgirl. The Skull Heart grants the wish by Making Parasoul take her place. The transformation is slow enough for her to train Umbrella to defeat her when she finally turns.
In Exiern Dragons are born looking like humans and gradually transform into their true forms after they mature. The protagonist's sidekick/like interest (she can't admit to more than that) Denver is a larval dragon, though he doesn't know it. His sister was well along in her transformation when she was last seen.
The Alchemist's transformation into Skeleton King from Super Robot Monkey Team Hyperforce Go! falls under this category. Fortunately, it gave him just enough time to turn his pet monkeys into the Hyperforce. What wasn't shown until "Golden Age" though, was that he was slowly aging. These were his last chilling words as he became Skeleton King:
Alchemist:"Now, the Dark Ones...(as Skeleton King) take my soul!"