This is one of those 'everything is the same, but A is B', in which Natsu is FTM because surely Zeref got something wrong while experimenting with things? Manga spoilers all around, so watch out. I will update this whenever I feel like, so I have marked it as complete even though it is not; its more like a series of drabbles and short stories centered around Natsu and Zeref anyways.
Zeref Dragneel was known as a prodigy through the magical community. Too smart, too powerful, too curious; he was feared and respected by those who had seen him in action, he was feared by himself and he was respected by his creations. He was, however, unsecure of many things through his life: is creating beings smart? Does the world spin left or right? Was the Leo Celestial Spirit annoying by nature or was that just with him?
Zeref Dragneel was sure of one thing in his life, and that was he had a little brother. Baby, male brother, who used to call him Selef and used to run around his feet naked when summer hit.
Zeref Dragneel does not quite know, then, why the baby brother curled up on his working space has a) pink hair and b) woman anatomy.
He can explain the pink hair as a side effect of the immense amounts of Dragon fire and ethernano he used to create and stabilize Natsu's gestating body while he (she?) was still in the fake womb he developed for all his creations. The womb had, expectedly, shattered upon Natsu's birth (it had been close to shattering when he created Mard Geer), giving Zeref no option other than cease his experimentation or create another womb, which he did not quite feel like doing. Instead, he recorded Natsu's birth in the book with his (her?) name and brought the sleeping apparent three-years-old back to the side room to check on his (her) health.
Natsu is a girl. That much is clear once Zeref runs a quick check up on Natsu's vitals and asks Alpha and Gamma to see Natsu's inner anatomy. The leader of the triplets tells him plainly the child is indeed female, with everything that implies, and also more human than all his other creations: Natsu is a fertile child girl , making Natsu the closest to true humanity out of all of Zeref's attempts for it.
He shrugs and, after asking Beta to care for his child sister , goes back to the experiment room to see what could have gone wrong . He had used Natsu's preserved body as a base for the new Natsu, with little few modifications to make his new sister fire-and-energy-resistant, so he does not quite understand what went wrong. The soul is proper, as well: it is Natsu Dragneel, still lingering from after his death, much like both their parents who constantly nag Zeref about doing the right thing and helping the world rebuild (he won't. He is way more worried about rebuilding his family than the world, but neither of his parents were willing to be guinea pigs to his experimenting). So if it is not a problem of the materials, it must be a problem with Zeref's modifications.
He pulls out Mard Geer's and Sayla's books to compare them to Natsu's, but then Acnologia's call sounds from closeby and he has to abandon his job. He knows he will never remember to go back to it, so he decides to just give up and pack up. He is done with this safehouse, anyways.
Alpha, Beta and Gamma help him skip cities, Beta carrying Natsu and Natsu's book (E.N.D., the cover says) while Alpha and Gamma carry everything else. They flee just on time to hear Acnologia crush the small town and start a long fight with Weisslogia, and flee just on time to coincide with Igneel's tired retreat. The King gives them a lift and, after bidding Zeref luck, sets off to locate Grandeeney.
The four of them settle in a new hiding place and, after recording his day and discoveries in the Book of Tartaros and the Book of Natsu, respectively, call it a day.
Girl Natsu will not speak. She ignores Zeref's teachings and denies Gamma's clothes. She tears apart the room Zeref has given her after Beta calls her 'such a pretty girl' and only relaxes once Alpha gives her a pale tunic for both genders. It is close enough to what boy Natsu used to wear in the old days, so Zeref chalks it down to familiarity and leaves it at that.
After the third time they have to run away from Acnologia in two months, Zeref starts planning a portable home (he writes his notes in the Book of Natsu, because the Book of Tartaros is his journal, even if the Book of Tartaros is what keeps Alpha, Beta and Gamma alive). The tenth time Natsu seems to be confused about herself, Alpha throws a quick disguise over her and promises he, now him, to teach it to him later. After the fifth time Natsu burns down a closeby location, earning him the nickname of devil child, Zeref clips the pages with the record of Natsu's powers and hides them behind a mid-powered seal.
The first time Igneel meets Natsu properly, he laughs and laughs, and then takes him away. Plan take-down-Acnologia is on its way, with four children and one Natsu being at the core of it. The first time Anna meets Natsu and Igneel with Zeref as a chaperone, she opens Gemini's gate and asks them to teach Natsu transformation magic since Igneel could not do it.
The first time the Leo Celestial Spirit meets Natsu, he becomes a lion and lets Natsu ride him into the distance, making Igneel, Zeref and Anna panic in the most logical way. Three demons, two dragons and five Celestial Spirits begin a frantic search for the Fire Dragon Prince -now apparent five-years-old-, only to find him climbing on Weisslogia, with Leo looking on in amusement.
The second time Leo kidnaps Natsu, Zeref does not panic -he is making a scarf out of Igneel's shed scales, carefully joining them together over a strip of Celestial fabric-, Anna does not panic, Igneel does not panic from where he is keeping watch over the Heartfilia heir. Baby Lucia naps calmly until Capricorn manifests, yelling something about Acnologia, Natsu and Leo; Virgo screams when Lucia is shoved into her arms and everyone is warped over to Natsu's apparent location by Zeref's half-mad magic.
Natsu is on Acnologia's arms, sleeping, and Acnologia is looking at him with something akin to interest. In the midst of war, Zeref screams himself raw at Acnologia, takes back his brother, and then screams himself raw at Leo after the Celestial Spirits, the demon triplets and Igneel manage to drive the mad human-turned-dragon-turned-human away. Never again , Zeref says, picking up the broken remains of his first children; never again will Natsu be alone with you, and Leo rages in rightful anger and promises to hate him forever.
Zeref is banned from the Celestial Spirit contract after he almost kills everyone in the area, including the Spirits and Igneel , and cleans the memories of Natsu off the Celestial beings' minds. No more Natsu for them ever again, he promises himself as he buries the remains of his three most loyal creations and locks the Book of Tartaros away. He hands the book to Anna much, much later, when Lucia turns five and claims she will marry Zeref.
The first time the five child Dragon Slayers meet, they make the cutest sight ever , and Zeref finds himself curling up next to Igneel and Grandeeney holding back squeals. His little family is the cutest and it is only missing Anna, on her mission to find the last key of Aquarius she is missing to work the Eclipse. So, Zeref watches as Natsu plays with a small Wendy, Gajeel pulls on their hair, and Rogue naps on Sting while Sting baby-blabbers to Natsu about something. It is adorable and he feels almost sad when he has to clear the memories of the event from them a couple years later, in their sleep, when they are carefully put inside the Gate to grow up alone four hundred years in the future.
Zeref kisses Natsu's forehead, whispers he will wait, how proud he is, how proud the triplets would have been; he kisses his cheek, whispers a goodbye and watches as his baby brother vanishes from his life for the next centuries.
Crying, he seals away the Book of Natsu, hands it to Anna, and disappears off the face of Ishgar.
Three decades later, Lucia cries on him because her mother is dead, her children are soldiers and the Book of her Older Brother Natsu has been stolen from her house. She cries on him because Acnologia has killed the land, the dragons are dying and the painting of her best friends is burnt to ashes.
Unknown years later, maybe two generations later, twenty years old Amadeus Heartfilia steals the Book of Tartaros with the help of Leo and Aries, beginning a chain of long and unfortunate events. Another unknown years later, the events come to fruition in the shape of plans are set into motion for Zeref's sake, without his knowledge from his growing nation of Alverez.
Centuries later, Layla Heartfilia opens a Gate, and the only spirit who can remember who asked for that favor is not present. Zeref watches from a safe distance across the ocean while the Spirits take the children to scatter them around Ishgar, and watches as the first thing Natsu does upon waking up is scream in despair.
Uncaring, Zeref covers himself with a blanket, wonders vaguely where Mavis is and falls asleep to dream about a childish boy-turned-girl-turned-boy running around his feet and calling him Selef .
Natsu Dragneel's first task in the morning had always been to recast the transformation magic on himself, take a long bath on the frozen cold lake in the mountains and then check if they had any food left from days before or if Igneel would have to hunt in the morning. Then, he would have the duty of lighting the fire (something that became easier by each passing day, his Fire resting inside his heart waiting for the spark), helping an already awake Igneel brush the leaves and branches off his wings, and cook his breakfast until it was warm (cooked meat was disgusting according to both Igneel and Natsu).
That had been how his childhood had gone, with no interaction with humans, unable to speak Common Ishgarian unless it was with a slight hiss and heavy rottics. Occasionally, a white dragon would come by to play-fight with Igneel, or another black one with a cute metallic sheen would come by to really fight with him. The feathered dragon would appear once in a moon cycle to give him a check up and lecture him about the expected changes in his body, and the dragon with the terrifying eyes would appear every three moons to teach him how to read. Natsu was raised by Dragons, for Dragons, to rule Dragons.
Natsu has vague, dreamy memories of five children and a black haired man constantly hovering ( family ), a woman with long golden hair and a saint-like smile ( family ) and a scary man full of scars who showed up to offer him a better life ( wrong ). Igneel had said those were memories of his dreams to have family and left it at that, but Natsu was never quite so sure because he also remembers a crowd of Dragons, so many Dragons. A flaming crown on Igneel's head and Dragons laughing and howling, clamouring for peace.
Unfortunately, there are no dragons anymore. No Igneel. No Weisslogia mock-fighting with Igneel, no Grandeeney telling him he is fine the way he is, damn it , no Skiadrum or Metalicana to steal Natsu away when they felt like it. No Dragons flying in the sky, covering the sun with their wings to give Natsu his wanted cloudy day; no Dragons that, every few weeks, dropped by with dead animals in their claws and barrels of fruit for them.
There are no Dragons, but there is a man called Gildarts, who looks at Natsu and picks him up and brings him to a huge building filled with life and people. There is a small white haired girl and a small red haired girl and an ice cold boy who reminds him of one of those children in his dreams ( Rogue ); there is an old man stamping a fairy on his shoulder, over the faded gray flaming crown that is his fake-birthmark. There is warmth and hot food and a bed and people willing to teach him how to be less Dragon and more human.
There are no Dragons anymore, but there is Fairy Tail. There is no Igneel, but there is a new family, and Natsu laughs and cries with them.
Lisanna finds an egg around Magnolia and brings it to the Guild, and the light blue bumps and yellow-white shell remind Natsu of Dragons . He steals the egg, because it is his Dragon , and curls up around it with all his heat every night. He has decided he will name it Happy, because the egg makes him happy, and it will make the whole guild happy as well.
At times, he acts like a dragon with shiny things and, at times, he acts like a female dragon with eggs. He realizes this when Lisanna and Mirajane and Erza come knocking at his door one morning to ask about the egg, and he snarls and fights and throws them out. His egg, his child .
Happy is born one morning that Natsu is still curled up around it -him-, and instantly latches on to Natsu calling him mama . It is on that moment that Natsu realizes the slight mistake on his part.
It takes him a few minutes to convince Happy that Natsu is not his mother , and that he does not want a child, really, but will live with him being a friend. Happy is confused, because Natsu smells like a mother, but he claims he is not, but accepts it as one quirk of human-dragons and does his best to not make a mistake.
Occasionally, Happy slips and calls Natsu mama . And so it is for ages to come.
NOTE: Originally, this started as FTM Natsu AU and it was just Jellal being like 'oh shit' and Zeref squealing about things, but then I got bored and lazy and whatever. So, here, have the Dragneel family's early life. You can ask requests for people's reactions, because everything is the same but people act slightly different.