Maybe he's too caught up in his work. Tony Stark is often depicted as a workaholic, so he could be so focused on his inventions and saving the world that he simply doesn't have time for his son.
It could be due to some past trauma. Perhaps something in Tony's own past makes it difficult for him to be a present father. For example, if he had a difficult relationship with his own father, he might unconsciously repeat the pattern with his son.
Another possibility is that he's trying to protect his son. He might think that by staying away, he's keeping his son out of the dangerous world he's involved in. But in doing so, he ends up neglecting him in the process.
Another possibility is that he underestimates the importance of family. Tony has always been focused on his own achievements and the big - picture stuff. He might not realize how much his daughter needs him until it's too late.
Maybe he doesn't fully understand his powers yet. Tony Stark is a scientific genius, but new powers might be beyond his current understanding. He could be worried that if he reveals them too soon, he won't be able to control them properly and might cause harm. So, he chooses to hide them while he studies and figures them out.
Guilt. For example, if he fails to save someone he cares about. He'll feel responsible and that could lead to him crying.
In fanfiction, emotional distress can also be a factor. If something really bad happens, like the loss of a loved one or the destruction of his work that he has put so much effort into, the shock and grief could be so overwhelming that he faints. Additionally, he could be suffering from some hidden illness that flares up suddenly and causes him to faint.
One possible reason could be that Shield has been corrupted from within. Maybe Tony discovers some dark secrets or unethical practices within Shield that make him believe it's a threat that needs to be eliminated. For example, if Shield was involved in illegal human experimentation or was secretly working with enemies of the state.
One possible reason could be that Tony Stark is being overly critical of Peter's superhero work. Maybe Peter made a big mistake during a mission, and Tony's harsh words in his attempt to correct Peter made him cry. For example, if Peter accidentally put civilians in danger and Tony scolded him severely.
One possible reason could be that he was forced to betray under some kind of mind control. Maybe an enemy like Hydra got hold of him and made him do things against his will. Another reason might be that he was trying to protect something or someone he loved in a very extreme way that seemed like a betrayal to others. For example, he might have made a deal with a villain to keep Pepper safe.
Maybe his own self - centered nature plays a role. Tony Stark has always been a bit of a playboy and a genius focused on his own projects. His daughter might seem like an afterthought compared to his latest invention or business deal.
One reason could be to explore the character's darker side. Tony Stark has been through a lot in the Marvel universe, and some fans want to dig deeper into his potential mental struggles, which could lead to thoughts of suicide.
One possible reason could be his excessive exposure to the arc reactor technology. The energy from the arc reactor might have gradually altered his DNA over time, causing him to become something other than human.