Disclaimer: I don't own nothing but the plot
Time Skip: Three Years
Tony Age 21; Natasha Age 23
As Natasha was listening to the deep, calm breathing of her partner and boyfriend, she couldn't help the feeling of euphoria that flew through her. The last three years had been the most stressful, but also the happiest of her short life. Of course there were some ups and downs in them, but that was too expected when a nearly emotionally broken assassin, who tried to repent for her sins through becoming an agent for the biggest secret organization in the world and a socially stunted billionaire/genius start a relationship together and they both being mutants just added to the daily chaos, destruction and craziness.
The three years had started relatively normal, well as normal as it could get. Juggling training, managing a company (Natasha as Tony's PA), inventing new stuff, going on a few missions and having a relationship with each other was surprisingly easy to handle. Of course some over lapping of duties and pleasure had helped as well, for example often Natasha would sit in Tony's workshops and write mission reports and look over complains and papers from STARK Industries, while Tony at the time would build, better or invent new things. Of course all this was managed pretty fast because of Tony's powers. They also planned their schedules to have at least two hours a day for personal stuff, mostly going on dates.
Through this work/pleasure rhythm they managed the first year nearly flawlessly, until they were called in for one mission that the both of them would never forget. It was also the mission were Tony first met Clint Barton aka Hawk-Eye.
Flashback
Tony and Natasha just had arrived at a small S.H.I.E.L.D Base for further information, when they were already shuffled into a quin-jet by Coulson and Barton. Apparently some scientist called Bruce Banner had experimented with something he shouldn't have and now turned into a giant green Monster, which smashed everything in its way and called himself Hulk.
Needless to say Tony was immediately a fan and nearly bounced off the walls in excitement.
Clint had looked at Natasha with a look that clearly said something like "Are you fucking kidding me"
When they had landed they had found a destroyed street and a giant, green monster running away from the U.S. Army. Tony had cackled like a maniac, winked at Natasha and sped off. With an annoyed sigh the others had took off after him in an attempt to catch up to them.
When they had finally caught up to them what they saw had stunned them. Tony looked like he was playing with the Hulk. Running with high speeds he dodged the punches and knocked the Hulk on its back and instead of getting more angry like the agents had expected, it stood up and ran after Tony, who had slowed down a little bit and let The Hulk "tack" him. Well he let the Hulk pick him up. Then they had looked into each other's eyes and The Hulk had reverted back Dr. Banner.
After that Tony had done what every sane person would have done. He offered Bruce an employment and "convinced" the U.S. Army and S.H.I.E.L.D that he would take care of him. Since then they had all become friends.
Flashback End
Natasha still thought it extremely weird that they had bonded that fast with each other. Even she herself who always was on guard around even friends, not to mention strangers, had thought of Banner as a trustworthy friend really fast.
In her time with Tony she had learned some things from Tony when it came to building and repairing things. She remembered quiet clearly how it had come to that the first time.
Flashback
8 Month after CARM(Captain America Retrieval Mission)
Natasha stumbled into Tony's lab ready to tear him a new one because he was causing things to blow up at 03.00 AM and quite frankly she was cranky because she hadn't slept very well the last few nights. Now on missions she wasn't too bothered by it, but now where she actually had some free time, she wanted to actually sleep god dammit. As she was about to kick Tony's ass he turned around, childlike glee clearly visible in his eyes. When he saw the frown on her face and after looking at his watch and realizing what time it was, his gaze dropped to the ground and he started to apologize "I am sorry for being thus loud. I didn't mean to upset you; it's just that I was really frustrated about something, so I threw one of my many projects at the wall and it shattered and exploded, but now I finally figured that something out that has bothered me for quite some time now which I would show you what it is that I have been working on, but it's all theoretical for the moment and I want to make it up to you and not bore you to death with boring theoretical chemical work and…" Tony rambled on for some time now and Natasha couldn't help the soft smile that crossed her features at her boyfriend's incoherent rambling.
Tony would have probably rambled on forever if Natasha hadn't shut him up in the best way possible, a swift kick to the shin. At his hurt expression she pulled him into a gentle embrace and kissed him full on the lips. When she pulled away Tony had a dazed smirk on his face while Natasha herself smiled brighter than the fire-body in the sky known as the sun.
Then she leaned in and whispered seductively in his ear "Ohh I know exactly how you could make it up to me."
Tony was smirking at her and leaning in to kiss her, when she suddenly pulled away and told him with a smirk on her face "Teach me how to fix and better my stuff."
Tony looked at her with an expression of disbelief on his face, until he realized how she had played him that made him glower at her playfully, while she just winked.
All teasing aside he taught her for two weeks and to their mutual surprise and pleasure she was quite adept at building, inventing and fixing stuff.
Flashback end
Natasha was quite happy with all this developments, but with all those good things happening to them, of course something bad had to happen. One year ago during a weapon presentation in Afghanistan Tony had been kidnapped by the terrorist organization called the Ten-Rings.
Due to some shrapnel near his heart and a magnet powered by an A.R.K.- Reactor Tony didn't want to use his powers, because he feared that if he moved at high speed the bullets would pierce right through the magnet and into his heart. So he stayed there for two and a half months and built himself the first Iron-Man suit with the help of a doctor called Yinzen.
Natasha had searched everywhere, with the backing and help of S.H.I.E.L.D, leaving STARK Industries to be managed by Obediah "Obie" Stan and Virgina "Pepper" Potts, whom Tony had personally promoted after meeting her through his driver, body-guard and friend Happy Hogan.
When the satellites had picked up the signal of a cave in a desert exploding Natasha had jumped into the next Quin-jet she could find and flew to the signal. What she found was Tony looking like shit, with a pained expression on his face and surrounded by U.S Soldiers, who were led by Tony's College Friend Colonel James "Rhodey" Rhodes.
After his return Tony called a press conference and published his intention to close the weapon manufacturing at SI (STARK Industries). This caused an uproar in the financial world, until in the next three day's Tony presented a detailed plan of the future and started the production of the first generation of STARK Phones, STARK Pads, STARK Motors and even a STARK Smoothie Maker for the smoothest Smoothies in the Smoothie world.
After that everybody who had doubted Tony quickly took back what they said.
After some investigation on Tony's part it turned out that Obie had bribed the terrorists in order to get them to capture Tony and kill them.
After they had figured that out Obie came and tried to beat Tony with one of his own inventions, which didn't turn out to well for Obie, because Tony was immune due to little ear plugs that absorbed every harmful sound in the air. (Dealing with explosions and shit he needed them quite often so he created himself and Natasha a few pairs)
After Obie flew from Tony's mansion he returned hours later in a bastardized version of Tony's first Iron Man Suit. Tony then revealed that he himself had built himself a far better suit than his Mark 1 model. Powered by an external core Tony didn't have to worry about his magnet running out of power. They had battled each other through the whole city, until they stood on the roof of SI, where Obie then crashed through the windows into the big A.R.K.-Reactor which proceeded to overload his Uranium powered until it exploded.
The day after that Tony had some S.H.I.E.L.D surgeons take out the shrapnel and through his powers the wound had healed in the next three hours, though he had to endure antagonizing pain.
Together with S.H.I.E.L.D they had decided that Tony would play the Iron Man for the public, to cover up his Agent work, thus Tony "arrogantly" revealed his secret to the reporters at the press conference the next day with the words "I Am Iron Man"