Being a superhero sometimes means you forget about the small dangers in the world, like disease. For Peter, this means he loses May to natural causes, not something he could ever save her from.
Unknown to him, May left custody of Peter in the hands of Tony Stark, who, even though he wants kids, has no idea how to actually raise one. With a grieving superhero teenager on his hands, Tony is going to have to figure it out quick, if he wants Peter to ever be able to move on and be happy.
Peter Parker's known for his entire life that things just don't work out for him. Not with an Uncle prone to violence and his apartment on the wrong side of run-down. He's made peace with that, used Spider-Man as an outlet for the hunger and bruises.
But then Tony Stark shows up, dressed in an expensive suit and carrying an internship opportunity. Peter can balance that on top of everything. He can keep a secret, he knows he can. And keeping this from Tony Stark won't be much different. Won't it?