Disclaimer: I do not own/am not associated with/make no money from the Avengers.

Warnings: This story includes references to underage sex, both because Tony started young and for a slightly more horrific reason that will become clear in the story but relates to his de-aging. There is no graphic, in text descriptions of sex in this story. There's also underage drinking, child endangerment, and what is technically, in hindsight, the torture and abuse of a child. The story will address these things but for the most part as things of the past. Also there will be some mention of fertility issues.

There will also be some cuteness to go with the angst. I promise.

It Begins

He had the best of intentions. It wasn't really his experiment to begin with. He had nothing to do with the malformed, horribly wrong things left floating in tubes or squirming grotesquely in their containment pens. In fact, Howard was part of the team that shut the project down. It was the sort of project that induced nightmares and showed every reason why such projects should never ever make their way beyond the hypothetical if they even went that far.

In fact, it was because he was avoiding the mass killing (not killing, disposal, those things had no true life, it was a kindness to terminate them) going on in the main labs that he instead looked into the numbers and equations and DNA that had gone into the project. He had a drink in his hands. Anyone who had seen the labs would need a drink after that.

It wasn't his fault that he was a genius, even if this was outside his usual field of expertise, even if the second drink made the world a bit fuzzy. It wasn't his fault that he had, in fact, been researching genetics as part of a personal project; something to turn tragedy and failure into numbers and equations, until all he could see was the science, not his wife's pain, not her flat stomach, not the empty cradle. It wasn't his fault that he could now see the abstract of what was being attempted. It wasn't his fault that he saw how it could work, be improved upon. That he understood the missing piece of the puzzle that had eluded all those other inhuman scientists because it took humanity to see it. They had wanted monsters, filling in gaps in the degraded DNA with monsters, and it hadn't worked, of course not, the results more sad than anything. It wasn't his field, personal projects aside, but Howard had always been a fast learner and he excelled in seeing how different parts fit together.

When he pricked his finger and entered his own DNA into the machine, the machine already set up, humming and waiting, he was just going to see if the blending worked. He wasn't going to actually grow the thing. He wasn't Frankenstein; he had principles. He did.

And it did work. But what he hadn't quite realized about the machine was that it wasn't designed to work in hypotheticals. Once it had the data, the machine did what it had been designed to do. And suddenly Howard had a new life, and it was tiny, too tiny to see, little more than a bundle of cells, but it was real. He could have ended it. Just by not touching the tiny glass tube that the machine had produced, the life would have had no way to grow. He could have smashed it right then. But then he really would have been killing it. It was alive. He could feel that it had worked. A human perfectly blended with an alien. Not just any human. A Stark.

Howard smuggled the glass tube out of the building. It wasn't difficult.

He told himself he was saving a life that would have been unduly terminated. He told himself that he had no intentions of using the information the embryo could give in the same way the scientists who created the technology had intended. Even if the child did turn out to be some kind of super soldier, Howard wasn't so out of touch with morality as to think that literally growing an army was in any way a good idea. He told himself that it was his duty as a scientist to discover what sort of being might grow. He told himself it was a way to give Maria what she had always wanted. He told himself many things.

He never quite admitted, not even in the most secret corners of his own mind, that maybe he had wanted a child. That ever since he got the news that having a child was impossible he had felt a cold ache somewhere inside. At most, he admitted to wanting a legacy.

Maria never asked questions when he told her they could have a baby. Howard never questioned whether this was a bad idea. Never mind the risks, that he didn't really know what kind of creature he was implanting inside her. Never mind that he had seen the results of the mistakes with his own eyes. It was his and it would be theirs. He believed in his own equations so hard that there wasn't room for things like doubt.

The baby was born ten and a half months later. There was no hospital, no birth certificate, no extravagant celebration welcoming the newest Stark into the world. The baby was born in secret with only Maria and Howard present and a team of highly discrete, highly paid doctors standing by outside the door and out of sight and, as there were no complications, ultimately never being told why they had been called to wait.

The baby looked human, small and pale and white with black fuzz on its head. It had Howard's features. Its eyes were something alien, something not quite right. Its ears were pointed, just enough to be noticeable. Maria smiled and called it Tony. Howard beamed. He named it Alpha Sigma for his case study and set about taking measurements.

He knew he was right. This was nothing like those monstrosities in the lab. This was perfect.

It wasn't until subject Alpha Sigma reached thirty six months that the first concern became apparent. In fact, it first showed up as something to watch at twenty six months and four days when certain measurements came back as virtually unchanged for the third measuring in a row.

Howard wasn't unduly concerned that the subject was registering only a slight increase of height and weight for three weeks, unusual though this may be in human infants. Subject Alpha Sigma wasn't human, after all, or at least not entirely, for all he looked like a healthy two year old boy.

"He's not growing; why isn't he growing?" Maria demanded, desperate and concerned while they watched the boy babble in baby talk to himself while carefully stacking colored blocks.

"He'll get a growth spurt soon," Howard insisted. But the boy didn't grow, or not very much. Then he wasn't two anymore, he was three years old, and suddenly subject Alpha Sigma wasn't just late hitting normal developmental mile stones, he was severely behind. He didn't just look the same at three as he had at two; he still acted like a two year old.

It wasn't that he wasn't smart and nor was it that he was clumsy. In fact, he was ahead of other children his age when it came to putting together puzzles or arranging shapes by size. The child had a natural grace and was much more at home in his body than a normal three year old. Howard speculated that this was at least partly due to the fact that most three year olds had to deal with a constantly growing body. Subject Alpha Sigma just wasn't growing.

He also had several cognitive delays, particularly with speech and social skills. It wasn't just that he wasn't really talking; he wasn't interacting properly with other people.

"It's because he isn't socializing," Maria insisted, "He should be playing with other children."

"Do you know what will happen if anyone learns he exists?" Howard demanded. Maria didn't, not really. As far as she knew, he was a revolutionary experiment in fertilization. If she ever suspected, if she ever ran her fingers over those pointed ears or looked into the alien eyes, she never said a word about it. She never commented that he didn't have any of her features, even though she was the one who carried him. She was his mother and that was that.

"So don't invite the parents," she said then, adamant that her Tony would not be isolated and hidden forever. "Who's going to listen to a toddler? Anyway, he can't stay hidden in a lab all his life; he's our son! You're his father, do something! Fix something so no one will notice if he's different. One of your ridiculous camouflage toys or something."

Howard went into his lab. He was on the edge of the future and peering beyond with the help of alien artefacts. Sometimes, he thought maybe he wasn't doing anything at all, that he had never done any of it. That there was something alive in the soft alien glow, something that wanted out. It was an easy excuse for why he created project Alpha Sigma. Being a father was enough of an excuse for what he made next. It would protect his son.

He had the best of intentions.

"It isn't a hologram," he told his wife later, years later in fact, while she stared at her son in wonder, running her fingers over his rounded ears, looking into eyes that very much resembled her own. Tony looked perfectly happy and content after the shock of the injection wore off, not at all like he was in pain or even aware of the change. "It's like if you take a negative and then make a photo of that negative," Howard continues, "only then you make some changes to the photo. And the negative is still there, but the photo is the real part, it's the part the world touches and sees. Alpha Sigma will grow now, you'll see, just like any other boy."

"His name is Tony," Maria scolds him with a playful shove. It's a long standing joke between them that started, as many jokes start, as a heated argument. In Howard's notes, he would always be Alpha Sigma. It was a way to protect him, as much as it had started as a way for Howard to protect himself.

Protecting himself from loving his own projects had never worked.

When project Alpha Sigma turned seven, he was roughly one inch taller than when he turned three. He had the vocabulary of a three year old, the social and emotional maturity of a two year old, the problem solving skills of a twelve year old and the math skills of an undergraduate.

He was introduced to the world as Anthony Edward Stark, age two, complete with birth certificate and heavily altered baby photos to prove it. Anthony Edward Stark continued to have speech delays up to six years of age when his many speech therapists' work finally paid off and he started speaking like any other six year old.

Anthony Edward Stark grew like a normal human child from childhood to adolescence to adulthood. Intellectually he was a genius. In just about every other way, Howard was distressed to find he still acted with the maturity of a young child. "Grow up," he tried to tell him, almost desperately. It came out harsh. The child with Maria's eyes glared back.

Howard told himself that his son was smart. He told himself that his intellect more than made up for his maturity. (He tried not to look too hard in the mirror to find out if that was true.) He told himself that his son needed a solid future and sure protection more than he needed coddling and playtime. He didn't mean to hold his son at arm's length but there was a part of him always waiting and watching, looking for the parts that were alien to shine through. Besides, Howard was a busy man. He had a business and projects to run. Tony had his mother. Tony had schools. One day, Tony would have everything that Howard could give him. Howard just had to build it first.

When Anthony Edward Stark was fifteen, he had sex for the first time. Because he was in a, for once age typical, rebellious stage, he was not particularly discrete. His parents found out. The whole world found out. Howard tried to console himself that the serum had worked, that it had even managed to send Tony through puberty and towards adulthood. He tried to console Maria by reminding her that Tony was really twenty years old, that he wasn't as young as he looked. Maria asked him how old he would look if he didn't have Howard's magical serum.

"He's just a baby, Howard," she cried, "He's a baby wrapped in a grown up body and he isn't ready. Talk to him."

Howard shouted at him. "You're a Stark!" he said. "You're ruining your reputation! My reputation!" he said. "You're underage and I'm worried about you!" he didn't say.

"You told me to grow up," Tony answered. Howard didn't know whether to be proud or furious. In the end he stepped back and added more notes to Alpha Sigma's file. The scientist in him remained fascinated by this development and he hated himself a little for it.

Howard called him his greatest creation, but never so Tony could hear. He never told anyone what Tony really was, not even Tony himself. And then Howard died, and Maria died, and that was really the end of project Alpha Sigma for all that Tony lived. It should have been the end. For a long long time, it was.

Author Notes: So...this is in response to this prompt which you can find at AO3 since they allow links.

I've written about five chapters thus far but it is a Work-in-progress (unless it's marked as complete, in which case this note is old, so ignore it). So I should be able to give fairly quick updates up to then, after which I make no promises. Apparently about five chapters is how long I'm able to hold out until the lure of feedback is too strong and I must start posting. I meant to at least hold off on this one until I finished the Monster Fighters, but since I've had about half the next chapter in that story written for months now and can't seem to find where I'm going with it well enough to write more...well, I might as well start a new story in the meantime. So...hope you enjoy.