In fanfiction, possible members of Tony Stark's secret family could include a daughter who has inherited his genius but has been kept hidden for her safety. Or a secret brother who has been living in the shadows and now emerges. There could also be a love interest that Tony has secretly married and they have a family together, away from the public eye.
It could be a long - lost son or daughter he didn't know about. Maybe a secret wife from his wilder days. There might also be a half - sibling that he never knew existed.
Maybe a brilliant biologist who has developed a way to enhance human physical abilities through genetic manipulation. A former S.H.I.E.L.D. agent who has inside knowledge of all kinds of secret operations and is an expert in combat and espionage. Also, a young inventor from a small town who has created some amazing but unrefined gadgets that catch Stark's attention.
A plot could also be that Tony creates a new secret identity to infiltrate a criminal organization. He has to completely change his appearance and mannerisms to blend in. This could lead to some humorous situations as he tries to act like a criminal while still holding onto his moral compass as Iron Man, and also some intense action scenes when his cover is nearly blown.
Yes, often there are many interesting plots. For example, the secret family might have to deal with threats from Stark's enemies while trying to keep their existence a secret. Maybe they have special powers or abilities that tie into the larger Marvel universe in unique ways.
One interesting fanfiction could be where Tony Stark's secret identity is discovered by an ordinary citizen who then has to decide whether to expose him or protect him. This creates a whole new dynamic as Tony has to deal with this unexpected threat to his double life.
His wife could be a former Hogwarts student he met during his own school days. She might be from a different house and they fell in love secretly.
In fanfiction, anything can be possible. Morgan Stark bringing Tony Stark back could be achieved through various means. Maybe she discovers some advanced technology her father left behind that has the power to reverse time or bring someone back from the dead in a scientific way. It could also be something more magical or otherworldly if the fanfic takes a more fantastical turn.
His secret family could also include an elderly relative, like a grandfather. This grandfather could have passed on some important family secrets to Snape, secrets that are related to a powerful magical artifact. And the family has been guarding this artifact for generations.
Another possibility is some disgruntled former employees. Maybe they feel they were wronged by Stark and want to get revenge. They know his routines and weaknesses well enough to plan a successful kidnapping.
Pepper Potts could be a big help. She knows Tony so well, and she could try to jog his memory by showing him things from their past together, like pictures or mementos. Rhodey could also be there for him. He could tell Tony stories about their military days and how they became friends, which might trigger some memories.
He would surely meet Black Panther. As the king of Wakanda, Black Panther would be the first and most important person Tony Stark would encounter.