I do not own Harry Potter or Superman, Marvel and DC do.
As of the time of posting, I am still writing this story, so have a couple of chapters to whet your appetite, then I'll try to update every Sunday.
What Has Gone Before
The Kryptonian Scientist Jor-El, having discovered that his homeworld was about to undergo a cataclysmic disaster that would destroy all life on it, chose to send his only child to a distant planet to save his life.
Escaping the destruction of Krypton, the young Kal-El landed outside the family home of the Potters, where he was taken in by James Potter and blood-adopted, replacing the stillborn Harry Potter and being given his name. Lily Potter was unaware of the substitution thanks to a memory charm placed on her by James and apart from Sirius Black, who had opened the transport pod and provided the ritual required for the adoption, no-one else knew that the baby was anything other than the trueborn son of James and Lily.
The next upheavel in his life came a bit over a year later when the magical terrorist, the self-proclaimed Lord Voldemort, heard part of a prophecy which he interpreted to mean that Harry was prophecised to defeat him. Seeking to break the prophecy, he managed to track the Potter family down, despite the secrecy charms protecting them, and proceeded to kill both James and Lily Potter. However, his efforts came to nought when he attempted to slay young Harry and his magic backlashed, destroying his body and causing his spirit to flee.
Placed with his relatives on his mother's side, Harry grew up unloved and effectively ignored. His cousin tried to bully him, but Harry's Kryptonian heritage proved to be a potent counter and with only a few demonstrations of his inhuman strength and toughness, Harry and the Dursleys reached an agreement, limiting their interactions to the bare minimum required while Harry raised money for himself by working as a paperboy for a local newsagent.
The status quo was shattered on the day that Harry's Hogwarts Letter arrived and Harry, not knowing of his heritage or inheritance, wrote back to say that he did not believe that he could afford to attend. In response, the half-goblin Charms Teacher Filius Flitwick set out to help Harry claim that which legally belonged to him and prepare for his years at Hogwarts.
During his introduction to the Magical World, Harry arranged to be emancipated, an act which shattered the protective wards around his former home. Alerted to the removal of the protections he had put in place a decade prior, Albus Dumbledore travelled to Little Whinging where he discovered that the assumptions that he had made about the Dursleys taking Harry in as a member of their family had been in error, a mistake compounded by the fact that the Dursleys had not known (or been able to collect) the stipend intended to offset the increased household costs. To make amends, Albus arranged for the entirety of the planned stipend to be delivered to the Dursleys, who promptly used it to move to a new home, one without the memories of their unwanted guest.
For Harry, life was looking up. He had located the site of his family's home (prior to it being burned down) and arranged for it to be rebuilt, but he also discovered something else. In a secret basement was the rocket ship that had brought him to Earth, a rocket ship containing an AI based on his father. After learning about his true origins, Harry concealed the rocket ship and prepared to go to Hogwarts.
At Hogwarts, Harry was sorted into Ravenclaw along with his two newest friends, Hermione Granger and Neville Longbottom. Together, they began their education in the ways of magic, aiding each other whenever they could and eventually offering help to others via a study group.
Harry and Hermione's friendship was cemented firmly after Harry rescued her from a Troll at Halloween. Although Harry used his more-than-human abilities to take down the Troll, Hermione finally decided that it had to have been a form of on-purpose accidental-magic, a conclusion that Harry happily went along with.
One of the ripples of the Troll incident was that Harry was allowed to try out for the Ravenclaw Quidditch Team (after three of the former players had been officially stripped of their positions), earning the position of Keeper. After his first match, his reputation for being able to block every single attempt at scoring spread throughout Hogwarts and beyond. Despite his abilities, though, it was Gryffindor that managed to secure the Quidditch Trophy.
Harry also discovered that a magical relic had been hidden in Hogwarts and soon had a fairly good idea of the obstacles protecting it. This proved useful when Hermione was dragged into the gauntlet by the spirit of Voldemort and its host, Harry was able to race through the challenges, almost without slowing, and defeat the Dark Lord with an uppercut that sent his borrowed body into the ceiling.
Due to being knocked out by Voldemort after she had failed to procure the Stone for him, Hermione did not remember much of what had occurred while Neville had been hit by an Obliviate that ensured that he didn't even know that Hermione had been in any danger.
To Harry's surprise, Hermione had managed to retreive the Philosopher's Stone and had concealed it from Voldemort. After she contacted the creator of the Stone, Nicholas Flamel, she received word that it was an enchanted fake and instructions on how to break the spells on it, leaving her with a lump of Mithril.
After the end of the first Hogwarts year, Harry returned to the Pottery, where the AI Jor-El was waiting to greet him, having rebuilt the mansion to incorporate concealed Kryptonian technologies.
However, the Wizarding World was still holding many surprises for the young Kryptonian…
With his ancestral family home not only rebuilt but augmented with Kryptonian technology, Harry made his entry into the political landscape with a summer ball during which he and his friend Neville Longbottom celebrated their birthdays. Soon after, it was time to head to Hogwarts, but his preparations were briefly interrupted by the appearance of a House Elf who warned him that he should not go due to a great danger.
Ignoring the warning, Harry took the Floo to platform Nine and Three Quarters, only for something to redirect him to another country. Fortunately, his Kryptonian AI Jor-El had finished constructing a stealth-capable shuttle which was promptly put into service to get Harry to Hogwarts.
At the sorting feast, Hermione's two pen-pals joined her in Ravenclaw. Although Luna Lovegood was expected to join the House of Wit, Ginny Weasley came as a surprise to all, especially her family.
The new DADA teacher, Gilderoy Lockhart, proved to be spectacularly incompetent and Harry called him out on it. Using Kryptonian technology to learn the magics of his ancestors, Harry was able to defeat Lockhart in a public duel, forcing him to resign and be replaced by Narcissa Malfoy who proved to be a superior teacher.
Proving herself very capable on a broom, Ginny joined the Ravenclaw Quidditch team as a Chaser.
After Halloween, Harry encountered a Basilisk, which he knocked out with a single punch before having Jor-El transport it to the Pottery. Once free of the control spells, the Basilisk accepted Harry's offer of a home, regular meals and conversation in exchange for helping to protect the Pottery and its grounds. The fragment of Voldemort that had been controlling the Basilisk (via possession of Luna Lovegood) was discovered and destroyed. Although affected by the experience, Luna soon recovered with the help of her friendsand even joined them in becoming Animagi.
However, Voldemort was not gone and another one of his Horcruxes allowed him to possess Lockhart. using his new body, Voldemort set a number of plans in motion, reaching out for new allies amongst the Vampires and Giants and striking down Igor Karkaroff, a former Death Eater who had betrayed him and moved to Bulgaria. Using the fact that very few knew that he had returned, Voldemort was able to access the Hall of Prophecies and gain full knowledge of the prophecy that Sybil Trelawny had made many years prior.
Around the time that Voldemort infiltrated the Ministry of Magic, harry discovered that his Godfather had been unjustly imprisoned. Using the laws of the Magical World, he had his Godfather publicly tried (with Veritaserum), during which Sirius Black proved that he was innocent and that it had been Peter Pettigrew who had betrayed the Potters. With his animagus form publicly revealed, Pettigrew was forced to flee to Voldemort's side.
Using a Vanishing Cabinet to bypass the wards, Voldemort had Harry kidnapped from Hogwarts and after binding him in magic-dampening manacles to revent him from being able to use his wand, he prepared to kill Harry in front of all his followers. However, Harry was able to use his wandless Kryptonian magic to create a null-magic field around Voldemort and his followers, following it up by using his heritage to break the chains binding him and escape was aided by a well-timed rescue party consisting of an axe-wielding Filius Flitwick,a gun-firing Remus Lupin and the Animagi Neville Longbottom, Hermione Granger, Luna Lovegood, Ginny Weasley and Sirius Black. While Albus Dumbledore was also present, the field that prevented external magic-use meant that he could only observe as the Death Eaters and their Allies were struck down.
Only a few of the Death Eaters managed to escape. Severus Snape (who was secretly working for Dumbledore) transformed into a bird to escape while Peter Pettigrew used small tunnels he had created on a just in case basis to flee. Lucius Malfoy didn't have a chance as he was killed when Voldemort dodged a fragment of metal thrown by Harry. While Voldemort managed to dodge, Lucius did not and the metal pierced both his mask and his skull. Despite his early escape, Voldemort did not survive for long as Harry used his own Animagi form to kill him.
With the excitement behind them, Harry and his friends returned to Hogwarts to recover. When the year ended, Harry learned that Severus Snape and the NEWT-level students he was teaching had managed something thought impossible, a potion that would turn a Werewolf into a Wolf Animagus. Remus Lupin was the first to undergo the procedure and prove that it worked.
Although things seemed settled, one of Harry's enemies had come into possession of yet another of Voldemort's Horcruxes…