Ever since he built the first Iron Man suit in a cave, Tony Stark has been a self-made man. He had a strained relationship with his parents until they died and left him their fortune, but it is Tony's intelligence as much as his inheritance that has allowed him to succeed. He consistently works to build better Iron Man suits, a better world, and a better version of himself, but the futurist Tony Stark has overlooked some huge secrets in his past.
In "The Secret Origin of Tony Stark" by Kieron Gillen, Greg Land, and Jay Lester, Tony learns that his life is a lie. In fact, Tony Stark is not even biologically a Stark, as his parents Howard and Maria actually adopted him after aliens meddled in their lives.
While traveling in space, Iron Man encounters a robot known as Recorder 451. The robot insists he needs Tony's help and has something to show the industrialist. Then Recorder 451 plays an old recording that shows Tony's father, Howard, alongside 451. Apparently, after Howard had impregnated his wife Maria, they learned their child would have debilitating problems and would almost certainly die in the womb. To save the future of his family, Howard acquired 451 to help save the child. The robot agreed, but there would be a cost. According to 451, humanity would be wiped out in thirty years by the Celestials. To prevent the god-like aliens from overpowering humanity, there would need to be a person smart enough to advance all technology on Earth: the Stark child.
Howard and Maria agreed to accept 451's help. Using Kree technology, the robot edited the fetus's genes, removing the medical problems while turning the child into a genius. However, there was another secret encoded into the fetus's DNA. The child would be able to activate the Godkiller, a mech capable of killing the Celestials. Then, at age thirty, he would die.
Howard discovered the additional genetic programming and removed it. Unfortunately, the boy was born with severe medical conditions. Howard and Maria named their child Arno, hiding him away from the world. To cover for this, they adopted a new baby, Tony, so that if 451 ever checked in on the family, there would be no evidence that Howard had undone the robot's genetic alterations. Arno grew to adulthood inside an iron lung, while young Tony grew up to become Iron Man.
This story profoundly altered the very nature of Tony Stark. While he had inherited his adoptive parents' wealth, his genius could not be attributed to his birth. In other words, Tony Stark really was his own man, a genius who controlled his own destiny. He reunited with his brother (who was even more of a genius) and Arno was finally able to leave his iron lung and move about with the help of various Iron Man armors.
However, things would get more complicated as future comics introduced new retcons. In International Iron Man, writer Brian Michael Bendis explored the identity of Tony's biological parents, revealing Tony's birth mother was a musician-turned-S.H.I.E.L.D. agent named Amanda Armstrong, while his biological father was a Hydra operative who had infiltrated S.H.I.E.L.D.
More recently, writer Jason Aaron complicated matters further. In Avengers: Earth's Mightiest Heroes #31, Stark encounters the devil Mephisto in a cave (after time traveling back one million years). Mephisto claims to be Stark's father, at different points implying that he was the real Howard Stark, that Howard gave Tony's soul to him, and that he was Tony's biological father. While the devil is far from a trustworthy source, the issue ends back in the present with Mephisto speaking to Howard Stark, who has mysteriously returned to life.
The never-ending soap opera of superhero comics frequently involves retcons and dramatic twists that undermine established continuity. Between Kree genetic manipulation, long-lost brothers, superspies, time travel, and deals with the devil, it can be difficult to keep the details straight. Ultimately, while characters like Arno have added layers to Iron Man's complexity, these stories have become so convoluted that most of these details will inevitably be undone with further retcons just so readers can keep track of everything.