While I can't recall the name of the fic in question (though you could probably find it through some intensive searching online. If you're a masochist), I do remember that it involved the Tenth Doctor (from Doctor Who) being kidnapped, turned into a vampire, and repeatedly raped and tortured by a possessive!vampire!Master.

There was also mpreg involved, if my memory serves me correctly.

Bob turning into Glitch Bob in Reboot was kinda weird.

Also Finn losing his arm in Adventure Time.

Not What it Appears gives Hermione really neglectful Replaced!parents, which leads to her and Harry getting "rescued" by Dumbledore and McGonagall's twin non-canon children, who then proceed to use a spell, which is so Glaurunging uncanonical that it is definitely capable of tearing the continuum asunder on its own, to turn them back into babies.

Now let's see... Hermione is eight at the start of this mess, which means that we are probably in 1987.
The spell turns them into 8 months old babies. So if you add about 10 years you get that... the events of HPSS (which are copied almost word for word) happen in 1997, a full Glaurunging six years later than in canon. Apparently, Voldemort is really patient now.

This thing also has the highest count of uncanonical relatives that I've ever seen: Dumbledore and McGonagall (talk about a crack pairing) have 8 non-canon children, and an untold number of non-canon grandchildren. McGonagall somehow had a son with Glaurunging Voldermort, who also had a son with Bellatrix. Said son then had a child, which gives Voldemort three too many uncanon relatives. And finally, Hermione is the biological daughter of Regulus Black.

and just for the record, here is the canon shattering spell:

Before me sits a child in shadow. I call the gods to bring him (her) to the light. Bring forth a new slate and begin again.

Erase the memories long since black
Erase the feelings never to come back
I am this child's father (mother)

I am this child's blood
From me this child shall learn
For me this shall mourn
From this day forth this this child is mine forever more

Return Harry (Hermione) to an age to start again to start anew and bring them to safely to my arms! .

In His little girl we have a potion gone wrong that drains most of Hermione's intelligence and gives it to Ron, which obviously would have made them really OOC if this ever continued. Said intelligence draining gradually leaves Hermione with the mentality of a toddler.

Her parents abandon her, she is given another highly uncanonical potion, which makes her phisically a toddler and then she gets adopted by Harry which convulutely turns him into a legal adult and there is the unexplicable mention of "magical adoption" making the child look like their adopted parents...

Yeah, I am definitely going to mission this thing after I am done with Rini's Horrible Death.

Madoka Magica Rebellion had some interesting stuff goign on, but turning poor Homura (who has her issues and surely is at least a bit obsessed with Madoka, but she's been though A LOT) into some sort of reality warping, flanderized, self-appointed Devil who remade the whole universe into one where Madoka is safe, against her own wishes, and justifying it with the power of "love" was pretty much headdesk material.

The even worse thing?

I'm not talking about a badfic. I'm talking about actual canon.

Twilight Sparkle becoming a hybrid of Godzilla, Destoroyah, and Spacegodzilla. I wish I was kidding.

The moment chosen for this change was somewhat logical, but after that the canon is drowned in an eldritch mix of beige prose, bad plagiarism and no logic. Not cool.

But seeing Fate Testarossa replaced to the point she tortures her own daughter was the only time badfic actually made me cry because of how bad it is.

Annie in Gunnerkrigg Court is a sweet, kind girl who is in a lot of pain for much of the story, trying desperately to deal with what happened to her mother and its aftermath.

Annie in Everybody In Annie's Forest is insane and a serial rapist and likely murderer. Also the phrase "fire cock" features heavily in proceedings.

I was Not Best Pleased by this turn of events.

It's Harry Potter again, but this time, he's thrown into Middle-earth and turned into a simpering, dewy-eyed toddler for reasons that are never satisfactorily explained.

~Neshomeh

... to Kimihito Kurusu from Monster Musume.

And it's used as an excuse for hard vore.

... either that or Lily Potter being a necrophile interested in Dobby's corpse. *shudders* That's in Valon and Kala's fourth mission.

I know I'm pretty much running the bashing of my old shame completely into the ground here, but that one replacement of mine was the first thing that came to mind - I'm pretty sure there are worse instances of derailment out there, but this was the most blatant I wrote personally.

For the uneducated, an online friend and I once co-authored a mega-crossover which included, among the long list of continua involved, The Incredibles and Jurassic Park, and the later chapters involved turning Violet (who's normally sweet, shy, insecure, and pretty snarky at times) into a ferocious mutant Tyrannosaurus with the abilities of camouflage, an impenetrable hide, and telepathic mind-speech. The last chapter of the fic before the epilogue actually had her outright ordering a villainous character replacement murdered, pun totally not intended, in cold blood.

The weirdest part? V-Wrex predated the Indominus rex by the better part of three years.

...into a Loli who dresses up like a Catholic schoolgirl. And then he gets magic surgery to become intersex and have Snape's babies. He also spends most of the fic depending on Snape to solve all his problems and he cries a lot.