Chapter 2
Snapes reaction: WHAT THE EVER LOVING FUCK!?! Followed shortly with: Stay the hell away from my precious! You touch my cat, (erm, child?) I. Will. End. You.
Dumbledore's reaction: nearly sobbing in relief of finding the (pawn) boy alive, followed by icy dread because his last four years of lies about the child's whereabouts have just been exposed before the entire school and several Ministry officials, including Cornelius Fudge, a weak man who will do anything to lay blame elsewhere (something that was exhibited when Peter Pettigrew was discovered and Sirius Black was cleared of all charges, where the spineless Minister was just barely talked into letting Bartimus Crouch take the fall for never giving Sirius a trial, instead of targeting Dumbledore himself.)
Emrys/Harry's reaction: why am I human again? I don't like this!!! My human will protect me until I am a cat again!
Dumbledore tries to take charge of the situation, but he is overruled by the Minister who has summoned pretty much the entirety of the DMLE. He only allows Snape to accompany the cat turned boy to Saint Mungos, because the boy refused to let go of the man.
An intensive health scan reveals the physical abuse Harry had suffered as a child, and despite not wanting to, he manages to tell Snape and an auror as much as he can remember of his time with the Dursleys, and exactly how and when he became a cat. All of this is said in stilted English with nanny yowls, growls, meows and hisses thrown in.
*Lore built specifically for this story: if an animagus procreates with an animagus (in their human forms, for those of you who require clarification) their child will be more likely to become an animagus themselves, far easier than normal wix. Lily, after learning James and his friends were all animagi, became one herself, a panther. She did it in secret with James, to surprise Lupin and the others, but before she could spend a full moon with the werewolf, she discovered that she was pregnant. After she had Harry and could safely transform again, they had to go directly into hiding, and suspicion that Remus might be a traitor had started cropping up, so they never revealed Lily's status to anyone else.
Harry, being injured, and locked in a trunk and terrified he was finally going to be murdered by the man, had managed to smash out the tail light on his uncle's car, something he read about in a crime novel he'd once read in the library while hiding from Dudley and his gang. After that though, he didn't know what to do, he wasn't small enough to fit through the hole, and he hadn't been able to finish the book to see what the kidnapped woman did next to finish freeing herself. When the car came to a stop at a light, Harry's panic fueled his accidental magic, and driven by the need to escape, and the belief that to do so, he needed to be small and quick, jumpstarted his animagus transformation, turned him into a cat and allowed him to fit through the small hole, and swiftly run away.
He might have transformed back after finding safely, but his body was too injured, and he'd expanded too much magic in the initial panic fueled transformation, so his magic went to work on healing him instead of changing him back.
After he'd been found by Snape and returned back to health, his new feline instincts attributed the man with safety, the first time he'd ever actually felt safe and cared for in his entire life, so his magic saw no need to change him back, as they were safe there.
In the course of four years together, the two of them formed some hybrid familiar/adopted family bond, their magic basically meshing well enough, that Snape unknowingly magically adopted Harry, who is magically now known as Emrys Snape, if not entirely legally.
End lore dump (for now)*
Tests at Saint Mungos, and later in the department of mysteries confirm Harry to be Snapes adopted son. A special collar is fitted to him, that will encourage Harry's magic to not spontaneously transform back into a cat, as his magic keeps trying to do so, and forcing him out of his animagus form too often can be traumatizing and damaging.
The summer is spent trying to rehumanize Harry, which is touch and go, especially when it comes to preparing him for schooling.
Sirius tries to gain custody of Harry at one point during the summer, but is shot down by Saint Mungos, the Ministry, Snape, and, well, everyone. Snape Hates it, but does allow concessions for highly monitored visits once Harry is deemed ready for it.
By the start of the next school year, Harry spends most of his time as a human, and can change back and forth between his forms on his own.
When he goes to get a wand though, none of the ones in Olivander's accept him. They discover though, that Harry can do wandless magic rather well, since he'd been unwittingly doing it as a cat for the last four years.
It's decided that Harry will be attending regular first year classes during the week and on weekends he would be receiving special tutoring.
The school year starts, and Harry is slowly adjusting. He's not too keen on how the other students keep harassing him, and the new Ministry evaluator, Dolores Umbridge, sent to audit the school in general, and Dumbledore in particular, has taken to sitting in on all of Harry's classes and tutoring sessions, constantly interrupting and making a general nuisance of herself, even going so far as to pass an educational decree stating students MUST use a wand to cast spells, and to do so without one is considered grounds for expulsion.
When that decree is announced, Snape finally loses his patience with the woman, and officially withdrawals Harry from Hogwarts. When a protest is launched, telling him he cannot have Harry live with him while he is employed at Hogwarts if Harry is not a student, instead of relenting and forcing Harry to use a wand that's won't work for him, he tenders his resignation, and leaves that very same day.
Less than a day at home, and he receives a letter from the Flamels, inviting him and Harry to stay with them in their house in America. The ancient couple had moved there for the year when Pernell was invited to hold a series of guest lectures at Ilvermorny & Salem, the two prominent American East Coast schools for witchcraft wand wizardry.
The two move to the States. Harry is allowed to attend some classes at Ilvermorny, and Snape is hired on as the new NEWT's level potion professor.
Things go rather smoothly for the rest of the school year, towards the end though, Harry starts having visions of Voldemort, and some guy named Barty. At first, they are written off as nightmares, which prompts Snape to decide to teach Harry occulmancy, both as a way to organize his mind, but also as a completely wandless sort of magic he can easily teach his son. Unfortunately, Snapes first few intrusions into Harry's mind reveal a genuine connection to Voldemort, and the nightmares are revealed to be true visions.
Snape consults with the Flamels. They recommend a healer friend of theirs that was a curse breaker for Gringots before she lost a limb to a Mayan temple and retired.
The woman found the horcrux in Harry, and suggested they commission a specialist to do an exorcism on Harry to get rid of the soul shard.
It's around this time that Sirius comes to visit Harry for the first time since they moved to America (he wasn't avoiding them, MACUSA just required him to be evaluated by a mind healer before he was allowed into the country, and his evaluation ended up leading to an extended stay in a magical rehab facility. He and Harry had communicated via weekly letters, up to that point, not that Harry was terribly interested in doing so, still holding a grudge against the man for how he'd treated Snape as a kid, but Snape insisted he at least try to foster a relationship with the man, because as much as he hates the guy, he loves his son, and does not wish to begrudge him a connection to his birth father, no matter how odious he finds the man.
Sirius arrives, and after a heated discussion with Snape, that ends up being mediated by the Flamels, Sirius decides to help, by throwing money at the problem and getting them the best specialist they can find.
By the middle of summer, Harry is Horcrux free.
Snape and Harry remain in America, Sirius and the specialist utilize the trapped soul shard of Voldemort to track down any others, and the dark Lord in question.
Sirius assembles a dream team of himself, Lupin, Bill Weasley who he contracted from Gringots, the specialist he hired to exorcize Harry, and a few others.
Within a year, they manage to track down all of the horcruxes, but before they can find the main soul bit, Voldemort is resurrected using the blood of Dumbledore, who had been caught unawares and been captured and used as a blood sacrifice to bring Voldemort back. After the ritual was over, Dumbledore was killed.
Snape knew the moment Voldemort had been reborn, as his dark mark had flared, though the magical summons was very weak, either because of distance, the reborn dark Lord himself being weak, or his connection to the man being weakened for some reason. In any case, Snape did not answer the call, but instead alerted Sirius and the Flamels. With their international connections, the Flamels got the ICW involved, but before a task force could be assembled, Snape and Harry were captured by death eaters.
The two were held captive and tortured for a few days, before finally being dragged before Voldemort and his assembled death eaters.
In the middle of the Dark Lord's villain speech, Sirius and a bunch of aurors show up, battle ensues, and it ends with Snape and Harry fighting Voldemort, and Harry delivering the death blow, by way of Sectumsempra, a spell invented by his adopted dad, who taught it to him with the express instruction to only ever use it in a life or death situation.
Most of the death eaters were apprehended by the aurors, Harry and Snape spent a few weeks in hospital recovering, and then returned to America where they applied for permanent citizenship on both the magical and muggle sides. They were granted it, and the two lived out their days with as little contact with the British magical world as possible (namely only Sirius and Lupin, who came to visit Harry at least twice a year, and managed to build a better relationship with him. Snape still disliked both of them, Sirius especially, but he tolerated them well enough for brief periods of time.)
Harry eventually graduated from Ilvermorny, though it was a good three years later than it should have been had he not accidentally become a cat. He went on to become a magizoologist, and traveled the world for a time, but eventually settled down in America to teach CoMC at Ilvermorny, alongside his father who was now deputy Headmaster of the school.