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So the Potters had a cat that we don't know what happened to. And when Voldemort comes to kill Harry, he actually succeeds.
Except Lily's protection kicks in, and like how Voldemort's soul broke into pieces and latched onto Harry's, Harry's did the same thing.
Minus the breaking, because his soul hasn't been split into pieces.
And by this point, the only being alive in the house is the cat.
So now Harry's a cat and he's very confused, to say the least, because he's still only a year old. He sticks around the ruined house and checks the dead bodies, and he's there when other people come to see what happened.
So the wizarding world thinks that Harry died with his parents. All of the Potters died on Halloween, and while they celebrate the downfall of Voldemort, there's no Boy Who Lived or anything like that.
McGonagall showed up at the house to pay her respects and cry a bit, and then she sees cat Harry watching her.
She knows Lily and James had a cat, and since no one's going to take care of him anymore, McGonagall adopted Harry.
Also, he gets some funny cute cat name, like Socks or something.
At first she thinks Harry's a normal cat, albeit one who's half a kneazle, and for a while his strange behaviors gets passed off as just kneazles being kneazles. But Harry's living with McGonagall in Hogwarts, and he watches her and sometimes other teachers teach their students, and eventually the boy in the mind of a cat wondered if he could do what everyone else could.
It was quite a shock when McGonagall found her cat doing accidental magic. Harry transfigured someone's clothes into a proper cat toy.
And now everyone's totally confused, because while cats can smell/detect magic and kneazles can figure out if someone's trustworthy, they can't actually do magic. Can they?
At first everyone thinks that they're just making it up, that the cat isn't actually doing magic, it's just McGonagall doing it for the cat for some random reason. But the incidents and evidences stack and eventually Socks the cat gets a magical checkup and they find out that it's somehow a horcrux, though with an intact soul? It's like the soul magically transferred bodies. Although there's a weird extra soul piece that doesn't belong to it somehow attached.
And Dumbledore suddenly remembered the prophecy that made Voldemort kill the Potters in the first place, the one that he didn't understand when Harry died.
Harry's soul had somehow transferred to a cat, although Dumbledore, McGonagall, and Snape are the only ones aware of the fact. McGonagall knows because it's her cat and Snape just found out by himself.
They make sure no one finds out about Harry, for obvious reasons, and McGonagall uses transfiguration to turn him into a human boy, albeit one who doesn't have a scar and looks slightly different than canon Harry. He doesn't look exactly like James, he's got Lily's face shape along with her eyes, his hair is neater, and he doesn't need glasses. Or McGonagall makes him not look like his parents at all for security reasons, one of those options. And Socks has been rechristened Harry McGonagall, McGonagall's son who showed up out of nowhere, unless they decided to call him Scott or something because Harry's too used to everyone calling him Socks and Scott sounds sort of like Socks.
Harry doesn't like being a human very much. He can see colors that cats can't and he feels so slow and clumsy. Plus, walking on two legs is weird, and what do you mean, he has to eat with utensils? And vegetables too? While McGonagall's transfiguring him into a human will last until she died, like how Slughorn had a transfigured fish that Lily gave him that only turned back when she died, Harry uses his magic to turn back into a cat whenever he feels like it. And he can turn back into a human too when he's asked. He's basically a reverse animagus.
Harry has a lot of catching up to do. He can't read, write, speak, or walk, and kids usually learn those things when they're young and pliable. Harry knows what words mean, at least, since he's been listening to everyone, and he can recognize some written words that the Hogwarts teachers wrote on the blackboard, but that's it. He's much more articulate when he's a cat, since he can understand and speak animal languages in that form. McGonagall can too when she's a cat as well, and sometimes you'll just see McGonagall and Harry hissing at each other for stealing the last rat or something. Animagi retain a couple of their animal traits as humans depending on how long they spend in their other form, since Peter still looks like a rat, and the same applies to behaviors. So slow blinking, tendency to sleep, etcetera.
Meanwhile, Dumbledore saw the shard of Voldemort's soul in Harry and realized that he must've made horcruxes. Dumbledore and McGonagall or Snape go searching for them and wormed out of Slughorn that Voldemort wanted seven, though he didn't technically make seven yet at the time of his death. Well, it was seven with Harry, but Voldemort doesn't know that and they know he doesn't know that.
Harry is more in the loop about the whole horcrux thing since he wants to know where his mom keeps going and McGonagall is less secretive than Dumbledore. Everyone's working hard trying to find ways to safely remove the horcrux from Harry without also removing Harry's soul from the cat, since Harry is a weird case.
They find the diadem when Harry snoops around the room of requirement and smells the dark magic radiating off of it. He's got kneazle powers since he's a part kneazle. Dumbledore finds the ring much earlier and he doesn't get cursed since someone else was with him at the time and stopped him from doing so. Sooner or later they also find the locket, though that one turns out to be a fake, but Snape figured out it must've been Regulus Black and they eventually find it at Grimmauld Place with Kreacher explaining what happened.
Dumbledore keeps the horcruxes somewhere safe in his office since they don't actually have a way of destroying them yet. He's also looking into ways of destroying the horcruxes without destroying the object, since it would help them figure out how to help Harry.
They try all sorts of things from old rituals to tying a rope around the horcrux and tossing it through the veil of death in the ministry and pulling it back, although that one won't certainly help Harry. Someone, maybe Snape suggests dementors, and even though everyone hates them, they're certainly good at eating souls, and Dumbledore uses the diadem and the cup and the locket to try figure out how to solve Harry's problem.
We don't actually know what the locket or the cup do, but maybe the cup gives you healing elixir or something, or the locket gives you directions to the chamber of secrets, since Slytherin had to have some sort of instructions on this. Or the cup magically duplicates whatever's in it or something. Who knows. We have full creative liberty here.
Harry also eventually finds the Chamber of Secrets since he wanders the castle a lot and can speak parseltongue even as a cat. Same way all animals can understand each other despite vocal differences, I guess. Harry makes friends with the basilisk, who's actually grossly misunderstood and pretty lonely down there, and is forced to do whatever Slytherin's heirs command her to do. She's basically a house-elf, and can only disobey through loopholes, which is why the only one who's died in fifty years despite how dangerous she is was Moaning Myrtle, and that was probably an accident since they didn't expect anyone to be in the bathroom when they left.
Also, I've decided that basilisks can turn off their deadly gaze, since it wouldn't make sense if they could accidentally kill their families or petrify themselves by looking at their own reflection. And the basilisk's venom is very helpful in horcrux disposal and another step in figuring out how to save Harry.
By the time Harry's eleven years old, he's gotten used to how to act like a human, though he still has some cat mannerisms. He's got a wand now, although he sort of figured out some wandless magic by just focusing on accidental magic really hard. And silent casting too, since cats can't talk. He's not completely overpowered, considering he's still eleven. It just came with having a strict teacher for a mom. And it's actually made him worse at casting spells with a wand since he's too used to not using a focus. Harry didn't really think he needed a wand, but McGonagall told him to get one anyway so he doesn't attract attention.
Also, Harry's already met the older students like Fred and George since Harry grew up at Hogwarts with McGonagall, so those kids already know McGonagall's mysterious son Scott and her cat Socks, which for some reason never show up at the same place as the other. Harry also doesn't really get along with Mrs Norris.
Harry meets Ron and Hermione at the opening feast after they're all sorted into Gryffindor, and they get along well. He also tells them about why they shouldn't go up to the third floor corridor, since he was there when they moved Fluffy in.
Although Fluffy wouldn't actually hurt anyone, he's just pretending to be savage to scare kids away. There's no age line because Dumbledore's letting the creative students take a peek at what they think is a dangerous animal and learn their lesson to not go to places they've been explicitly told not to go.
Snape doesn't hate Harry as much since he was basically there when Harry grew up. He's still biased, but that's because Harry's a Gryffindor, not because Harry's a Potter. The Slytherins mostly think McGonagall's going to spoil Harry because he's her son, but if anything McGonagall's even harder on him than anyone else, since he's bad at wanded magic.
Harry also figured out that Scabbers wasn't a rat very quickly. From the instant he was close enough to smell him, actually. So he went to his mom who did the spell to turn animagi back into people, and with some veritaserum from Snape, they find out about Sirius' innocence.
Snape is extra mad at him, by the way, since it's Peter's fault that Lily died.
Sirius gets a trial and he comes to visit his godson along with Remus. Remus also knew about Harry's furry situation, I just forgot to mention it until now. Sirius finds it hilarious that Harry's a cat and basically an animagus at a year old, beating all the Marauders put together, and so dubs his Marauder name as Socks. Harry's never escaping that name, not that he really minded being called it in the first place.
Also, McGonagall on Harry's request takes Ron to Diagon Alley during one of the holiday breaks to get a new pet since since Scabbers turned out to be a human. Harry and Hermione tagged along too for friendship bonding and to maybe get an owl, but Hermione ended up with Crookshanks instead and Harry gets along with the new cat splendidly.
Since Harry knows Snape and he thinks Quirrell smells bad, the trio suspect him of stealing the philosopher's stone instead, and Harry goes straight to his mom with his suspicions. It's hard to sneak into the school with Voldemort on the back of your head when Harry also has Voldemort in his head and knows what he smells like.
Quirrell got sent to Azkaban since he wasn't possessed long enough to die. Rita Skeeter got intrigued did some digging because she wanted to know how Hogwarts lost a teacher within the first few weeks of the school year. Sure, there's the curse on the position and everything, but this early?
So she finds out about Voldemort possessing Quirrell and leaks the news to the world, letting them know that Voldemort isn't dead.
The world is in a tizzy, since everyone believes Rita Skeeter no matter what she prints. The ministry is under fire for letting Peter go free while they wrongfully imprisoned Sirius, and now this. Hogwarts gets a similar treatment for hiring Voldemort as a teacher.
To save face, Umbridge gets sent to replace Quirrell. She's not denying that Voldemort's back, since everyone knows that fighting Rita Skeeter is a losing battle, but she's cutting corners that shouldn't be cut just for the sake of saying she did something. Everyone hates her, of course. She tried to pet Harry when she saw him in cat form, and he immediately scratched her as much as he could get away with before running away. He didn't get in trouble for that, and ten points were mysteriously awarded to Gryffindor that day with no one sure why.
Unfortunately, escaped Death Eaters also believe Rita Skeeter, and soon they're looking for Voldemort. Voldemort's trying to get a body back, but he still thinks Harry is dead, so he doesn't go after him, at least.
Umbridge eventually gets some horrible thing happen to her because of the defense against the dark arts curse, and Lockhart shows up as the new teacher. Remus would do it, but he's busy on Order of the Phoenix business.
Also, at some point Harry explains his whole furry situation with his friends, since he trusts them implicitly. He's not going to keep secrets from them just for his own benefit.
Meanwhile, Voldemort still required a body, and he's unsure about the prophecy about the one who would defeat him since Harry's supposedly dead but he's the reason why he doesn't have a body anyway.
But Voldemort decides that if he doesn't know the answer to a multiple choice question, he'll just have to circle all the answers, and he has the diary sent to Hogwarts to kidnap Neville, the other potential chosen one.
Ginny still gets the diary, but the basilisk who should get a name destroys it personally before anyone got hurt or possessed, even Mrs Norris. Harry had never smelled a more evil book before.
Also, Harry managed to figure out a way to order the basilisk to never obey other orders again unless she wants to, so she's free just like Dobby. Although I'm not quite sure how Dobby escaped the Malfoys in this version, since he never met Harry since he thinks Harry's dead along with everyone else.
Angry that his plan failed, Voldemort has Malfoy try to kill Dumbledore as punishment like in book six, and he orders the Death Eaters to literally grab Neville as he's coming off the Hogwarts Express with his grandmother right there. Everyone does their best to stop them, but they're unsuccessful.
Harry, in cat form, only manages to leap onto Neville just as they're disapparating away, and so he goes with them.
They end up in a graveyard and Harry scampered away, and the death eaters don't pay him any mind since they just think he's a cat and they don't want to waste time killing a random animal when Voldemort's waiting for them. So they just get ready for the ritual.
Harry watches as the Death Eaters put Tom Riddle Senior's bone, someone's hand, and Neville's blood into the cauldron, waiting for the right time to strike where he won't get himself and Neville killed. While they're all distracted, Harry uses magic to surreptitiously unbind Neville from the gravestone he's tied to.
Then someone brings out baby Voldemort, and Harry just knows he has to do something.
Accidental magic kicks in, and something in the potion changes, so when Voldemort tries to get a new body, it comes out... a little different than how he expected it.
Maybe he's deformed, maybe he's a muggle, maybe he's a girl. Whatever happened, Voldemort's immediately really mad at whoever it was that messed up the potion, and while all the Death Eaters are cowering and blaming each other, Neville and Harry escape in the commotion, though Neville didn't get his wand back. Don't worry, he'll get a better one from Ollivander's that didn't belong to someone else previously.
The two boys run away until eventually they find a wizard whose floo they can borrow and they get hugged by their respective guardians. Aurors got sent to the graveyard along with Dumbledore, and they briefly fought Voldemort, but he retreated to recuperate and most of the Death Eaters escaped.
However, Dumbledore couldn't help but notice how protective Voldemort was of a strange snake that Harry said smelt weird.
Also, Nagini can smell Harry too, which is a problem. The Death Eaters are on the lookout for cat animagi now.
Dumbledore finally managed to perfect something that gets rid of Harry's horcrux, and they spend the rest of the war trying to find Voldemort and kill Nagini.
But Malfoy's still trying to kill Dumbledore, and eventually he leads the Death Eaters into the castle, and Voldemort's with them.
A curse takes out Lockhart and they figure out later that he's a fraud, but that's not important right now.
Voldemort, gleefully, orders the basilisk to come out and destroy all his enemies.
Except when she comes, she no longer obeys his orders.
In one clean stroke, she swallows Nagini whole, getting rid of the last horcrux, and her fangs close tight around Tom Riddle.