Cat-astrophy

In the mad dash to escape Harry's letters, Harry has a bit of accidental magic while they are making their way through Cokeworth and turns himself into a cat. He wanders lost for a few hours before he holes up under a pile of wood to wait out the rain.

Snape finds him the next morning when he arrives home to check on a few things. Harry is soaked through, obviously starving, as well as severely injured from the beatings he'd taken every day he got more letters.

Snape, a secret cat lover, takes the skittish kitten with him back to Hogwarts, cleans it, heals it, feeds it etc.

Harry, confused with his human brain muted and running off mostly instinct takes a week to warm up to the man. After he does though, he declares the man his human and decides to never leave him.

Snape feels drawn to the cat, and instead of taking it to an adoption center like he would normally do, he decides to keep his new cat with him at Hogwarts, names him Emrys, partly for it's emerald eyes, partly after Merlin who was a Slytherin.

As an animagus, Hagrid is unable to track Harry down behind the wards on Snape's house. When he tells Dumbledore he cannot find Harry, he consults the book of names to see what address was last printed for the boy, and goes to 4 Privet Drive himself.

The Dursleys are not yet back so Dumbledore Faffs about for a few days before he is finally able to get in contact with them, looking at Vernons memories, he sees the man beat Harry severely over the letters and then stuff the unconscious boy in the boot of his car with the luggage before driving to the ocean.

Dumbledore fears the man may have murdered Harry and dumped his the body at sea.

Can't tell anyone though, has to hide it, and keep looking for the boy, maybe he survived, or even escaped, since the man does not have any memories of dumping the boys body.

Tries to get the book of names to write Harry another letter, but it won't anymore, because Harry is already at Hogwarts.

School year starts, Dumbledore hadn't found Harry, so he tells the story of Harry receiving special training for his own safety. Is out of the castle more than in it for most of the year.

Harry befriends Fluffy.

Somehow finds the stone. Leaves it in Severus' shoe as a birthday gift. Severus is confused and slightly displeased, but decides that if his cat can find the damn stone, then it's obviously not safe at the school, especially with Dumbledore gone so much, presumably training the absent Harry Potter. He takes it to his house and puts the house under fidelis until the end of the school year when he can send it back to the Flamels.

Harry spends the year exploring the castle, befriending most of the animals that reside in the castle and aren't food and basically forgetting he was ever human.

Summer comes again and Harry is left behind at the castle while Snape returns the stone to the Flamels.

He tells them how he ended up with it, and how the head master has spent the year too busy to be in the castle most of the time, so Severus decided to hide it and return it himself.

The Flamels had not trusted the real stone to Dumbledore, but rather a fake.

Snape was embarrassed, but then gratified when Nicholas asked him to collaborate on a project with him. They do so for a week in person and then continue to do so via owl correspondence over the next few years.

Second year starts with another announcement that Harry Potter is still in hiding receiving special training for his own good, and once again, Dumbledore is gone more often than not, leaving the running off the school mostly to McGonagall, who delegates her deputy duties to the other three heads of house to share.

On Halloween, Mrs Norris is found petrified next to a message saying the chamber of secrets has been opened. The incident is handled as a cruel prank, until a muggleborn boy, Colin Creevey, is found similarly petrified. Unfortunately, that incident happens while Dumbledore is in the castle, and he stops the rest of the professors from summoning the Aurors to investigate properly.

That year for Snape's birthday, Harry leaves him a giant serpent shed, draped across his bed, and the first sight the man sees when he wakes the morning of his birthday. After a brief moment of panic, and then a half a day of research he determines it to be the shed of a basilisk. It was enough to clue him in to exactly what the monster of Slytherin was, and working with Filch McG and Flitwick they managed set up disillusioned roosters in stasis primed to crow in the presence of a serpent in every hall way and painting. Thanks to that they were able to kill the basilisk the next time it came up to kill, and catch Ginny Weasley with a diary absolutely drenched in black magic. Flitwick took the diary to his cousin at Gringots who was a curse breaker, and they were able to destroy it.

The week before term ended, Harry brings Snape Lockhart's wand, going to return it he finds Lockhart trying to obliviate a student with their own wand. Calls the aurors, and the student tells them they had found out the man was a fraud and decided to confront him instead of turning him into the authorities(Gryffindor obvs) The rest of the school year is quiet, and Snape and Harry start their summer out in spinners end, with a brief jaunt to Germany to visit the Flamels. Their visit is cut short however by an urgent summons from Dumbledore and they are forced to return to Hogwarts only a few weeks into their vacation. When they arrive back in England, it is to learn that Sirius Black had escaped from Azkaban. Snape vehemently voices his displeasure over this fact, and goes on several rants about the horrible man, and how he tried to murder him when they were evil children.

Emrys does not like this, and resolves to protect his human from the horrible man.

Shortly before the end of summer, Emrys meets a crazy dog near the forbidden forest. He feels strangely drawn to the canine, and the two strike up a strange friendship.

When the school year starts, Emrys makes another new friend, an Orange cat one of the Gryffindor's has brought with her. When Emrys introduces his car friend to his dog friend though, his dog friend turns into a man, and the man tells his cat friend about the rat man hiding in the Gryffindor boys dorms.

Emrys listens to the man and skinks of with his cat friend after. It takes the two of them some time, but they finally manage to track down and catch the rat man. Emrys decides to take the rat to his human to deal with, because the dog man was giving off some bad vibes once he turned into a human.

So for his birthday that year Snape gets a rat dragged onto his super plate. Thinks, at least this time it it some thing normal for a cat to leave their human, but then the rat wakes up, and tries to get away. Emrys goes after it, and nearly kills it, only for it to turn into Peter Pettigrew. In the middle of the packed great hall.

Remus nearly wolfs out.

Dumbledore is out of the castle, so the Aurors are called.

by the end of the school year Sirius is declared innocent.

"Where the hell is my godson?!?"

Dumbledore tries to waffle, special training, for his own safety etc, Sirius not buying it, but blocked at every turn trying to find the truth.

Fourth year, goblet of fire.

Dumbledore, hoping to use it's ancient magics to track the boy down, enters Harry Potter as the only candidate of a fourth school.

Name that comes out though is Emrys Snape.

Dumbledore thinks he screwed up somehow, and everyone else thinks it's some kind of prank, someone entering Snape's familiar into the tournament.

Still, the rules of the competition state he will need to "compete" so they plan a bit extra, for it. Snape thinks it's stupid, but reading the magical contract, it's apparently necessary, if he doesn't want to risk losing his own magic through their familiar bond.

The dragon doesn't even notice Emrys stealing the kitten sized egg from its nest as the cat it too small for anyone to see. (Emrys new favorite toy is the miniature animated dragon. He takes it everywhere with him, and the enchantment on it lasts far longer than it should, though everyone suspects that is Snape's doing.)

the original plan to have the second task take place in the Black Lake are scrapped, as there is really no way for them to make it cat friendly, so they change it to a scavenger hunt through the Forbidden Forest for the "thing they will miss the most" Emrys finds Snape first, but gets docked points for being carried out of the forest by Severus.

Emrys is able to get through the maze really well, and makes it to the cup, but it's a portkey and doesn't work for animals, so he just curls up and takes a nap inside waiting for the next person to take hold of it.

He is declared joint winner with Cedric Digory.

At the award ceremony, Emrys catches a shiny bug and decides to give it to Snape as a gift, because he uses beetles in his smelly potions and this one feels extra magical, but Snape, wary of what happened the last time Emrys brought him a living present, decides to test it with a spell to force an animagus to turn back into a human, just in case. The spell hits both Emrys and Skeeter.

In tattered rags, putting his every scar on display, Emrys Snape transforms into Harry Potter, and promptly hisses his displeasure before scrambling behind his human to hide in his robes.