Jarvis dies before Nattie turned three, and her cries when she can't find her Jay breaks his grieving heart. That's when he starts to build an A.I Jarvis he would build in all their homes so she'll—they'll—never have lose Jarvis again.
When Jarvis' soothing British tone first talks to Nattie after Tony finished installing him into his computer and hooking him up to cameras, speakers and mics that he puts almost everywhere in his workshop/Nattie's playroom, his bedroom and Nattie's as well as their shared hallway, Tony's heart feelings like it's going to burst with the beaming smile that takes over her chubby face before she rushed around hugging Dum-E, Nanny, Tony's legs and finally the walls—saying simply that she was hugging Jay when Tony, completely bemused, asked her why she was trying to hug the wall.
Tony didn't miss the almost embarrassed tone that Jarvis used when he thanks 'young Miss Nattie'.
Though he's later annoyed when Jarvis and Nanny team-up to make sure he eats, but it is something that the old Jarvis did with Nanny so he only half-heartily tried to ignore them.
It's only December 16th 1991 that Tony realised how Nattie's family consisted only of Tony, Dum-E, Nanny and Jarvis.
It's the day he got the call that his parents have been killed in a car accident, the day he crouched down to where Nattie's playing with a Circuit board and tells her that Howard Stark, their father, is dead.
It's the day when Nattie looked at him confused, and questions him on who 'Dad' was, and Tony felt a chill go down his spine when he realised that Howard had completely left Nattie in his care and Tony didn't notice that he was never around for them.
Tony felt strange when he had to use a picture so Nattie knows who Dad was, and had to explain that he wasn't coming back like Jarvis. She's not bothered by this as she never knew this 'Dad' person anyway.
Howard may have not been around much when Tony was a kid, but Tony still knew he was his father. Nattie didn't have that though, Nattie had only been surrounded by robots and Tony for all four years of her life.
She hadn't even met Rhodey though Tony isn't sure able telling his best friend—only human friend—about Nattie as Tony had never had to share Nattie before and isn't comfortable with telling him. Not now at least.
It's the next day after Tony had signed the paperwork to make him CEO, shaken too many hands and had too many bulbs flashing in his face before he tries to leave only for Obie to, horribly jokingly, ask who was waiting at home for him.
Tony went still as he stared at Obie, only half-aware of the winces on the members of press and broad of directors' faces, and realised that dear old Dad had never told one of his oldest friends about Nattie.
He could see the moment when Obie realised what he had just asked the newly orphaned man, see the apologises on his lips, and cuts him off with a cocky—fake—smirk and a 'special girl' for the answer. It was the start of his playboy antics that would be spread across the tabloids for years to come.
While Tony may trust Obie, he didn't trust anyone enough to share Nattie with them. It would be years down the road that Tony would be thankful with that decision, because he hated to think what Obie would have done if he knew that Nattie was his sister and how close Tony really was to her.
For Christmas, Tony built Nattie a robot dog, basing the size and shape off a Yorkshire terrier, and says it's called Howie. He tries to ignore that part that tells him that a dog will never make up for Howard, her father, being in her life.
He kept focus on the happy laughter when the small dog-bot does the tricks that Nattie commands him too.
Logically Tony knew that Nattie would have to go to school despite the fact that Nattie was a genius like their father and himself. Logically Tony knew that he didn't have the time to teach Nattie everything himself, logically knew that Nanny couldn't teach Nattie things that she would need, and logically knew that Nattie needed to learn how to interact with people.
Logic had no effect on the panic at the thought caused.
So perhaps Tony over-reacted because of that.
He set up his own school under the Maria Stark Foundation, used that foundation to give money to other schools so not to bring attention to the Stark Institute that he was going to enrol Nattie into.
It was only when he was completely secure with the security of the Institute before he enrolled Nattie into it, hiring a driver/bodyguard to drive her to and from school.
Tony did not mope when Nattie went to school the first time, he didn't constantly ask Jarvis for the time, he didn't throw a ball for Howie to chase just to shut up the constant whining, he didn't watch as Nanny swirled around the house picking up stray toys and dusting, and he most certainly didn't watch Dum-E sadly hold Nattie's favourite teddy before fleeing to his office at Stark Industries.
He was completely focused on his paperwork, on the accounts for Stark Industries especially.
The spitfire red head that stormed into his office later that day, waving around his completed accounts' paperwork as she ranted about the mistake he made and with his bodyguard clutching their eyes in pain behind her, pepper spray in her free hand kind have pointed out that he hadn't been focused at all.
He ended up telling Nattie about his new PA over the Spaghetti Bolognese that Nanny cooked them later that night, making the six year old laugh at the thought of her big brother scared of a raging red head.
Tony moves them to Malibu after Jarvis informs him of some reporter trying to follow Nattie's car in the morning. He buys a plot of land on the coast with access to its own beach, and hires people to build the house of his dreams while setting up another Stark Industries building in California.
The new house has better security, Jarvis' eyes and ears built in everywhere so nothing could happen in the house without him knowing.
All of Nattie's rooms were connected and locked against strangers—it was easier for Nanny to move around the house. There was a secret garage that is built especially for Nattie to be able to easily leave and come from the house without reporters knowing.
Nattie announced after it's finished and they can move in that it looks like something out of an alien movie.