Welcome to the Miracleverse! AKA, the Disliked Ships AU, but I don't use this as a platform for hate. While the universe is slightly… twisted, they are all options that could have happened in the main TFIMverse. They're a chance to do things with the… standard ships that people have, and using them in new ways, as well as a platform for interesting characters. I want to do some different things with the designs, so I may note the standard designs I tried to avoid with each design. These designs have been done for… an embarrassing amount of time, so expect a lot of the designs at once, I finally decided to upload them. But, since this is a canon character, and I did it in the past few days, that doesn't quite apply. So instead of 'what I did different' with their children, I'll explain my design choices for each of them!
Spike's design in this AU is different than my standard design due to growing differently than in the TFIM universe, due to his dragon growth due to one of the seven sins (just a hint of lust and wrath) being accelerated. His design is based on his adult design in 'Secret of My Excess' and he wears a ring the color of Humdrum's belt and gem, and his bow is the same one from 'Owls Well That Ends Well', just.. well, he's much bigger… And for Spike, a special thing… I know this is a filibuster, a bit, but I wanted to logically calculate Spike's age so I could get a feel for exactly how questionable Spike and Rarity's relationship is. It's important, in some ways. And I just like showing my work.
First off, establishing something; The Mane 6 are all at least 21 by season 2, the cider that the Apple Family sells is alcoholic, meaning they all have to be 21, at the least. This, even if you don't accept the cider as alcoholic, is supported by the fact that they're all in the same age range, and Rarity is old enough to open her own store, live on her own and support herself financially. So we have established that they're all in their mid twenties (any older and we'd get into the ages where their parents would be more old looking and also their behavior doesn't fit people in their thirties). My headcanons stand with Pinkie and Twilight at 21, Rainbow Dash at 22, Applejack at 24 and Fluttershy and Rarity at 26. These all fit in the category set up. With that established, we have the question of Spike's age. We know that the very minimum age Twilight could have entered Celestia's School; 5, since there'a Magic Kindergarten, which would make Spike 16 at most, but that's not backed up by other facts in the show; we know that Twilight and her friends got their cutie marks around the Cutie Mark Crusader's age, which is around 10-12, not 5, meaning that Twilight had to be around that age, making Spike 10-11 at the beginning of the show, supported by the fact that Spike was not emotionally or physically able to fit in with teenagers, making it logical that he is not one, an analogy would be of Dipper and Wendy's friends in 'The Inconveniencing'… And around 3 years have passed since season 1; making Spike 13-14 at the point the Miracleverse began. 25 years (approximately) have passed since the divergence point, for the record, making Rarity 51* and Spike 38, with Rarity knowing Spike since he was a minor and knowing that he was romantically attracted to her. It's up to you if you find this distressing or at the least mildly questionable, but they're the calculations.
With that over, Spike is the husband of Rarity and father of Miracle, unofficial and adopted son of Princess Twilight Sparkle, Spike was devastated by the destruction of the Crystal Empire, not just because they loved him for saving the empire in the first place, but because the moment the Crystal Heart shattered was when he broke down and cried for the cousin he never had. The Crystal Ponies looked up to the brave and glorious Spike for strength and realized even he wasn't able to be strong at the death of the baby princess. Of course, it was never actually his fault, the Crystal Heart was falling apart, but it was accidentally the straw that broke the camel's back, and it took Twilight almost a year to convince Spike that it wasn't his fault, that he didn't cause it, that Shining Armour and Cadance weren't gone because of him. It wasn't his fault, but he still blames himself secretly, and the many Crystal Ponies that live in the Empire that still idolize him, he helped them escape, he lit a fire to help them stay warm, but he still felt as though he was responsible, and it still hurts him.
He and Rarity started seeing each other behind Twilight's back, not out of illegality, but for fear of upsetting her; she was already in a fragile emotional state, and she was always on edge. Spike was 21 and Rarity was 34, and while ponies looked at them oddly, for Spike was still an awkward, gangly looking mess of a dragon who looked like he was only 17, they kept quiet. Ponies knew Twilight was on edge, who didn't? Anybody who knew who the Crown Princess of Friendship even WAS knew she was a wreck about to crash given the slightest chance, so everypony agreed it was best to let Twilight… not know about her surrogate son/sibling, whatever Spike was to her, it wasn't ever stated, and Spike wasn't entirely sure either, about Rarity's tryst with him. It just wasn't wise to anger the mare, truly. But Ponyville still gossiped; it was no secret that the young dragon had loved Rarity since he was only a child, how long had they been hiding it?
Rarity heard ponies whisper about her being a cradle-robber or cougar, and they had many awkward stares, after all, grooming a foal (which everypony who knew Spike thought of him when he came to ponyville) into a relationship was a crime, taboo.. but they truly hadn't started dating until Spike was 21, after his first night of drinking as an adult, the two got…. tipsy.. It happened almost a little something like this, though of course, Spike hadn't been gone, they had simply decided to celebrate the final coming of age in a pony's life (something Spike felt more attached to than his heritage) together, and… things were done and said. It wasn't their first kiss, of course… that had happened 10 years ago, but this time, Rarity meant it. And this time, she didn't have any hesitations.. even if afterwards, she questioned what she had been thinking, the warm fire of Spike's chest kept her there. It was risque, questionable… exciting. Rarity found the star crossed romance exhilarating, the attraction between a predator and prey, the fact that she finally could see him as what he was, a dragon, a fire breathing creature with claws and teeth and.. oh, the danger that could be imagined sent shivers down her spine. She had read books about Marewolves and Bat Ponies and the illicit romances between them and a normal mare, but she never realized how much she wanted a relationship like that until she had one.
Of course, Twilight found out after three years of them dating in secret (too busy with her own family to take care of her.. well, other family) and she… they hadn't been wrong to assume she'd blow up. How dare Rarity keep something like this from her? How dare Spike not trust her enough to tell her? Did Rarity really think that Twilight would be alright with this? She had known all along that Spike had a crush on her, how could she toy with Spike's feelings like that? Didn't she realize that Spike was only 24, sure, it wasn't as illegal as it could be, it wasn't even illegal, but how long had it been going on? Did Rarity always like Spike like this? Was Rarity preying on her surrogate son all this time?… No matter how much they assured her that they had only been in love for three years, Twilight was paranoid and tried to keep Spike away from Rarity, but Spike… well, Spike was an adult now, he could make his own romantic decisions, and he didn't have to listen to Twilight if he didn't want to. And he didn't want to. So he moved in with Rarity, fueled by anger that Twilight would think such terrible things about Rarity, that she wouldn't believe him about it. The anger and resentment balled up in him and he grew just a bit, every day, as he let anger fester… but Rarity comforted him, he slowed.
Eventually, Twilight apologized to both of them and for her behavior, though their relationship was now strained, Spike was her.. son?.. she had raised Spike, and Rarity was the one Spike loved, as well as a close friend, so she made her peace with her fears of Rarity taking advantage of Spike's romantic naiveté, unable to accept that Spike might have grown out of it… Had he?.. When Rarity became pregnant some time after, Twilight became a whole new whirlwind of anxiety… Rarity should have expected it; this would be her grandchild?… whatever their child would be, it would be something Twilight would panic over… she knew why, and she felt pity but being doted on by somepony who wasn't her husband, it was a bit overbearing, from the months of fussing to the baby shower where Twilight bought an egg incubator for Rarity, just in case she laid an egg, even though ultrasounds had confirmed that the child would be a live birth, Twilight insisted upon it. Just in case… after all, Rarity was facing some challenges in her pregnancy… normally, while uncommon, dragon and pony crossbreeds existed, they were aided by the natural magic that helped mares have children with other mares, the love magic that formed children, something was wrong, the love magic that should have aided them didn't work, and their child was to be born a hybrid without the protection of magic, something that was dangerous for the mother and child, but Rarity and Spike both agreed to keep their child.