New Timeline:
Given this is now a mix of Two Stories.

• Unofficial Sequel to:

"If Wishes Were Ponies".
https://www.fimfiction.net/story/406279/if-wishes-were-ponies

• Official Sequel Up, by original Author.
"If Wishes Were Ponies, Book 2".
https://www.fimfiction.net/story/484183/if-wishes-were-ponies-book-ii

• I take some inspiration from:

"Magic School Days".
https://www.fimfiction.net/story/371039/magic-school-days

"Hazy Days and Magical Ways"
https://www.fimfiction.net/story/477026/hazy-days-and-magical-ways

###

New Timeline:
Given this is now a mix of Two Stories.

● 1st Year.

• The events of "If Wishes Were Ponies", exactly as they happened.

● The Summer, just before 2nd Year.

• The story starts to take inspiration from "Magic School Days". Starting with the winter break, becoming the summer break in this universe.

• The Weasley kids spend some of their vacation with the Apples.

• Twilight creates a spell, to give wizards Pony forms. Which is in addition to their Animagus form. Later, she even perfects the spell into a ritual, anyone could use. Although the Ritual depends more on personality, and innate magical ability, as to what pony tribe your new form would become. As opposed to what you might have wanted. Even Squibs can be put through this ritual, and manage to transform at will. Most of the people, close to the ponies, were put through the ritual.

• On Dumbledore's "Suggestion" to the Princesses, Harry's herd spends some of their vacation with their Gryffindor year mates. Both short visits to their homes, on Earth, and the wizard-kin coming to Ponyville. With them visiting Equestria, being insisted on by The Princesses.

• Snape is allowed, by Dumbledore, to have various Death Eaters arrested, for child abuse.

• Without the protections of these key Death Eaters, as they held a large amount of political power, Starlight Glimmer is able to move forward. Rallying the wizards, through the press she now owns, to reopen investigations into all accused Death Eaters, who got off due to an Imperius Curse claim. The Minister is forced to bend to public opinion.

• Starlight is able to get muggle borns to claim the house seats, of the Death Eaters that were arrested. Even claiming a seat for herself.

• Lord Sirius Black dissolves the marriage contract, between Lucius Malfoy and his wife Narcissa. Lord Black proceeds to reabsorb Narcissa into the black family.

• Draco, and his mother, were moved into Black Manor. Accepted by her cousin, Sirius Black, Lord of the Black Family.

• Sunburst evaluates Twilight's ritual, and creates an amulet which will allow for temporary shifting between pony, humanoid form (using Equestria girls coloring for ponies), and an Earth magical being form (Centaur, House Elf, Goblin, Giant, or other beings straight out of a D&D Monster Manual). That works on either side of the portal. A side effect of this amulet is it acts more as a training focus. Meaning, after prolonged use, it will no longer be necessary to transform. He begins selling them in a shop in the Earth Embassy, but at first only to magicals and Squibs, due to the statue of secrecy.

• Sirius writes up a new marriage contract, between Narcissa and Remus Lupin. As they were childhood friends, and clearly still have feelings for each other. Draco throws a fit, seeing himself in even further disgrace at becoming the ward to a Werewolf. Sirius retaliates by writing a marriage contract for Draco. Marrying him off to be the trophy husband of the filly, Diamond Tiara.

• Princess Luna teaches the werewolves of Earth, to embrace what she calls their "gift". Allowing the Werewolves to keep their minds, without need of a potion. As well as how to turn at will, without pain. To live in Harmony with the wolf inside them.

• Harry Potter becomes cousins with Draco, when Lord Black sleeps with Princess Twilight Sparkle, and their magic recognizes them as married. Harry is hesitant, but Spike is thrilled to have a dad.

• Feeling bad about not sharing her husband, in a proper herd, Twilight introduces Rainbow Dash and Pinkie Pie to Sirius... and with Sirius being Sirius, they "mate" that very night. The ministry, and their family tapestry, recognize them as married.

• Daphne Greengrass buys some of Sunburst amulets, as gifts for herself and her little sister Astoria. However, the amulet reacts badly with Astoria's blood curse, and she nearly dies. Sunburst is able to stabilize her, before bringing the family to Ponyville hospital to be treated. Where, much to the family's amazement, the ponies are able to treat the blood curse. Even cure it.

• Daphne goes to stay with Rarity while her sister is being treated. However, when the family comes to reclaim their daughter, a misunderstanding occurs with the Greengrass parents, and Rarity thinks they are courting her. When this is revealed, after much embarrassment, the Greengrass realize they don't mind the idea of entering a "Herd" with Rarity.

• Discord giggles with delight at all the chaos being unleashed, and it is revealed he made the first portal, saving Harry's life. He has been working with the gods of Chaos, Choice (AKA "Free Will"), and even Justice, to manipulate things on both sides of the portal. Discord gets tired of acting behind the scenes, and starts interfering more directly, much to the displeasure of the gods of Earth, who have a long standing policy of not interacting directly with mortals. Discord exposes magic to the entire world, by posing as a freelance reporter, and sends irrefutable evidence to all the major news stations around the world.

• Magic is exposed to the entire world, and most of the muggles take it surprisingly well.

● 2nd Year at Hogwarts.

• Dozens of teachers, from Equestria, are brought to Hogwarts, in order to teach, or simply act as teacher's assistants. With Zecora becoming the new potions instructor, although Snape maintains his roles as "potion master" (meaning he is in charge of making most of the school's potions), and Head of Slytherin.

• A thousand of Equestria's best and brightest foals, are selected to go to Hogwarts. However, other students have their parents pay for the privilege. Such as: Button Mash, Rumble, Dinky Whooves, Diamond Tiara, Silver Spoon, and over 4 dozen others. Diamond Tiara, Silver Spoon, and Rumble, are sorted into Slytherin. Where Diamond is named "Slytherin Primus" by the sorting hat.

• On the train ride to Hogwarts, Discord gives Luna Lovegood a Crystal bat pony form. The first of such Hybrids.

• Diamond forms an Alliance with Applebloom's herd. And orders Draco to respect it.

• Sweetie Belle is discovered by an Earth Unicorn mare, who decides to adopt the filly.

• As the first month goes by, Snape becomes less resentful of being replaced as a teacher. As he gets to know Zecora, and begins to fall in love with her. They sleep together, but it isn't for a couple weeks, before they learn their magic bound them as a married couple. Zecora, not wanting to keep Snape to herself, introduces him to Applejack, and a Bat pony guard the Zebra is friends with. It takes the entire year, before the mares can convince Snape to form a herd with them.

• Draco gets more used to being a "Trophy Colt" and finds he enjoys not only Diamond's cunning, but the way she pampers him. Draco even slowly forms a rough friendship with Applebloom's herd, including Harry.

• Harry discovers Elly is a changeling, and after discussing it with his herdmates, ask Elly to join their herd. While promising to keep her secret.

• On further discussion with his herd, Luna Lovegood is added as well. As Harry feels protective of her. Due to how she is being bullied by her Ravenclaw Housemates.

• Twilight steps in, saying 7 mares is far too many for one Stallion, and insist the fillies either find some other colts to add, or kick out all the humans. Harry's herd respond to this by asking Neville if he would like to join, over breakfast in the great hall. This results in the other Gryffindor 2nd years asking if they can join to... Twilight is shocked they are able to build such a large herd, with so many Stallions. Not even minding that they ended up adding more girls.

• Needing 1 more girl, for their herd to be legal. (Given herds at least 2 mares for every Stallion). They ask Daphne Greengrass.

• The boys are Harry Potter, Ronald Weasley, Neville Longbottom, Dean Thomas, and Seamus Finnigan. While girls Hermione Granger, Ginny Weasley, Lavanda Brown, Parvati Patil, Luna Lovegood, Elly de Ripp, Daphne Greengrass, Apple Bloom, Sweetie Belle, and Scootaloo.

• Dumbledore discovers Elly is a changeling, but, given Elly's record at the school, including once saving Harry's life, decides to allow Elly to stay in attendance, and doesn't inform the Ministry, or the ponies. Similar to what he did for Remus, when he was a student.

• The Ministry, fearing how involved the ponies are becoming in their government, declares war. Discord steps in, and scares the piss out of the Ministry. Getting them to agree to leave the ponies alone.

• Starlight is found by the ponies, helping rebuild / reshape wizarding government. Twilight manages to convince her to abandon her plans to conquer Earth, and Starlight becomes Twilight's first student of Friendship.

• Voldemort's diary consumes the soul of a Slytherin Child, and teen Tom Riddle leaves the castle. None the Wiser.

● 4th Year of Hogwarts.

• Harry's name comes out of the Goblet of Fire, and he is forced to compete in a deadly tournament. This causes an interdimensional incident, when Twilight learns the Goblet will kill Harry if he refuses to compete. Even though he didn't put his name in.

• When Harry wins the tournament, Voldemort uses the opportunity to capture the teen. Ransoming him back to Twilight, in exchange for all Ponies knowledge of magic. Including their fusions with muggle technology. All 4 Princesses agree to the deal. Allowing Voldemort to leave peacefully, as ponies are creatures of their word.

● 5th Year of Hogwarts.

• Few believe Harry that Voldemort is back. And the Ministry tries to silence him. Even sending Dolores Umbridge into the school, armed with Blood Quills.

• Dolores Umbridge uses a Blood Quill on Harry, and Twilight finds out. She immediately sends her guard to Hogwarts, arresting Umbridge. Then sentencing her to a thousand years in the Chaos dimension. Assuring her, Discord has agreed to keep her alive for that long.

• The Ministry does not react well to Umbridge's arrest. But back down when Twilight informs them she would gladly go to war over this. As the Wizarding Government appears to be truly irredeemable. Celestia is seconds away from declaring war, herself.

• Voldemort attacks the ministry, with ponies magic guns.

• The Ministry begs for Celestia's help, too which she refuses. Instead, rounding up magical civilians (from wizards, house elves, Goblins, and dozens of other species). Which she brings into Her embassy. While leaving the Ministry to fend for itself.

• Celestia orders all the ponies out of Hogwarts. Along with the herds they have formed. Including all the families, and even friends of, those herds.

• The Ministry panics at all the people leaving their boarders, and destroy the portal at the pony Embassy.

• It turns out destroying the portal was orchestrated by all gods of fate, from both dimensions. As their own attack against Discord. Casting him out of their dimension, and reversing all the transformation magics he used to turn others into ponies. However, the gods of Choice, Chaos, Justice, and magic retaliate. Rebelling against their non-interference policy, and revealing themselves to mankind.

• Meanwhile, Sunburst, who was one of the ponies that got trapped on this side, starts mass producing his amulet. With an unintended side effect being ponies, who use it to turn into humans, now keep their pony coloring, even in human form.

• The gods of magic begin teaching wizarding owls how to travel between dimensions. With the ponies arming the owls with pouches (containing a large luxurious room inside). Unfortunately, the gods warn these are more limited then portal travel, as they are still bound by some rules, and won't just bless the owls with abilities they don't naturally possess. Owls are the Messengers of gods. With wizards (being distant descendants of demigods) having just taken to using them without realizing all they are capable of. The owls can travel to other dimensions, but they can't rewrite anything they bring with them to fit that universes laws. So traveling can be dangerous, as the ponies that go back might get dimensional sickness.

• Voldemort learns what owls can do, and doesn't bother with the testing the ponies are doing. Merely sending an army of Owls across dimensions, to recruit the ponies greatest enemies. Given Celestia doesn't hold power over the human's sun, the more dangerous races of Equus form an alliance with Voldemort. Deciding to fight their battle on Earth. World War 3 breaks out. With ponies being unwilling to call for reinforcements, as they don't know the long term effects of owl travel.

● Season 6 of Friendship is Magic, during what would have been Harry's 6th year of Hogwarts.

• After much testing, ponies confirm Owl travel is safe, and start sending ponies back and forth between dimensions.

• Discord returns to Earth, and he, and all of Equus gods, get pulled into a war of their own. As many of the Earth gods are rebelling against their Elder God, causing a full out civil war.

• Elly is discovered to be a changeling, when she lays several eggs. Twilight is pissed, as Harry is the father, and Twilight believes Elly used her son. Possibly even replaced the real Elly. However, Harry reveals he's known she was a changeling, since their second year at Hogwarts.

• Spike meets Thorax, and befriends the young changeling. Twilight learns, for certain, that the issue is Chrysalis, not the Queen's Children.

• Elly used her Philosopher's Stone to create trees which produce love honey, in berry form.

• Chrysalis escapes into the human world, through one of Voldemort's portals, and attempts to destroy the love honey trees, as well as kill the new Queen Elly and her grubs. Dumbledore saves Elly.

• Thorax returns to Chrysalis' hive, and leads a Rebellion. Which ends with him ascending into a Changeling Queen, and all his siblings transforming into their "Reformed" changeling forms.

• Elly learns, due to being on Earth, there isn't enough magic in the human dimension, for her to properly transform. Instead she only slightly mutates. Her holes fill, her exoskeleton changes into darker pastel colors, although her mane still looks like colorful thick spider-webs. All the grubs, in their eggs mutate similarly. Even all of them gaining Spider-web manes and tails. Unfortunately, due to them partially transforming, they can't complete it. Not even if they return to Equus. Elly doesn't mind too much, as she thinks the darker colors, and keeping her fangs, is a nice look.

• Other Changeling Queens follow Thorax lead, and transform into their reformed state. However all the Queens turn into a different kind of bug. No two the same. They become a wide variety of different types of bug horses. But with all their Drones, workers, and Warriors, matching the same species as their queen.

Changeling Species
* Doppelgangers (Elly).
* Love Bugs (Thorax) .
* Forest (Based on Lovestruck Derpy, with wood branches and moss growing out of them).
* Moths.
* Crickets.
* Bees.
* Spiders.
* Wasps.
* etc.

● What would have been Harry's 7th Year of Hogwarts.

• The first eggs, of a reformed Changeling Queen, is hatched. However, they are the same species as their mother, and the changelings realize they are dozens of subspecies, each their own proper race.

• Harry joins the fight to defeat Voldemort. Mostly to save Equestria, and her Allies.

• Harry learns Voldemort found a new way to be immortal. Without any Horcruxes left, he had himself bitten by a Vampire, and then created a more traditional phylactery. Turning himself into a hybrid Lich / Vampire. In order to eternally maintain his beauty, and gain true immortality.

• Harry goes on a hunt for the phylactery, knowing, if he destroys it, Voldemort will instantly die.

• Harry finds the phylactery, but it is trapped in a dimension that never moves... if he goes in, to get it, he can destroy the phylactery... but will be lost for all eternity. Harry jumps in without a second thought, but joined by both his friends and family. Including the herds of: Snape, Draco, Twilight, and his own. Even Elly joins. As Well as the Black family.

• The group sleeps in a luxurious expanded suitcase (Even bigger then the one from "Fantastic Beast and where to find them"). Which is also were Elly's grubs are raised, and hatched. Elly is largely providing everyone with a base of operations, and keeping everything neat and tidy. As she doesn't want to risk her next batch of eggs, which she is currently pregnant with. As Changeling Queens can have sex once, and start laying a dozen or more eggs, once a month, for hundreds of years.

• The group had to go through hundreds of traps, and battle various dangerous creatures. But they manage to get to the final chamber, only to see Voldemort is waiting for them.

• An epic Battle erupts, with Harry being the one to destroy the phylactery.

• From there, the herds discover a portal back to Earth, and are finally able to get back home.

● 1 year after the war.

• Thorax takes Spike as his Consort, who is already in a relationship with Gabby. So they form a herd. With Gabby being the first Griffin to join a herd, in over a thousand years.

• Thorax starts laying eggs of his own.

• Twilight opens up her "School of Friendship", however she uses teachers from all races of their dimension, and attempts to promote interspecies cooperation. Rather then teaching friendship, the school is designed to encourage it. Most of the Mane 6 act more as guest Speakers, and occasionally oversee field trips. However, they aren't teachers. Rarely stopping by, as this is more Twilight's dream.

• The war of the gods ends as well. With all gods that rebelled being cast out, and taken in by Equus.

● 3 years after the war.

• Celestia steps down and Twilight becomes ruler of Equestria.

• Starlight inherits the School of Friendship.

• Starlight joins a herd with her friends Maud Pie, Sunburst, and Trixie.