There could be a rescue mission. The other Avengers might find out about Tony's kidnapping and split into two groups. One group might believe Steve has a good reason and try to negotiate, while the other group might go in guns blazing to rescue Tony. This would lead to a lot of internal conflict within the Avengers.
After the kidnapping, Steve and Tony could have a series of intense conversations. They might start to understand each other's points of view better. Maybe Tony reveals some secrets or past traumas that make Steve realize he's made a mistake. Or Steve could explain his motives in a way that makes Tony see things from his perspective, leading to a possible reconciliation and a new alliance between them.
The story could develop with Tony trying to reason with Steve. Tony might use his intelligence to talk Steve out of whatever his plan is. He could point out the flaws in Steve's reasoning or show him evidence that he's been misled.
Will might find a way to escape on his own. Since he is also a Cipher, he could have some hidden powers or tricks up his sleeve. Maybe he manages to outwit Bill and gets away, which then sets up a cat - and - mouse chase between them throughout the fanfiction world. The story could also take a darker turn. Bill might start to torture or manipulate Will, changing Will's personality or making him do things against his will. This could lead to a conflicted Will, and the other characters might have to deal with this new, changed Will when they finally find him.
Often, it might show them trying to find their own identities again. Tony could focus more on his Stark Industries projects, pouring all his energy into creating new technology. Steve, on the other hand, might go back to a more solitary life, perhaps traveling around to help small communities in need.
At first, their relationship would be very strained. The guilt would make it hard for them to even look at each other. But as time passes, they might start with small gestures. For example, Steve could leave a note for Tony apologizing for some of his actions. Tony, in turn, might respond in a similar way. This could lead to short conversations, which gradually get longer as they start to open up more about their feelings.
At first, it might be a bit rocky. Tony, being used to his own space, might feel smothered by Steve and Bucky's over - protectiveness. But as time goes on, he'll start to see their good intentions. Steve's moral compass will inspire Tony to be a better person, and Bucky's loyalty will make Tony feel secure. Eventually, they'll become like a real family, with Tony looking up to Steve as a father figure and seeing Bucky as a cool older brother.
The kidnapping could be a turning point in their relationship. They might start to see each other in a different light. Steve could see Bucky's desperation and the lengths he would go to protect him, even if his methods were wrong. Bucky, on the other hand, could realize how much Steve means to him through the guilt of kidnapping him. This could lead to a more intimate and emotional bond between them as they work through their issues together.
Well, it depends on the nature of the fanfiction. In some cases, the kidnapped character's friends or allies will come to rescue them. This can lead to a big battle or confrontation with sans. If sans is being controlled by someone else when he kidnaps, the rescuers might have to figure out how to free him from that control as well. Sometimes, the kidnapped character might also find a way to escape on their own, and then they have to decide whether to get revenge or try to understand sans's motives.
The story could develop in many ways. If it's a more angsty fanfiction, Annabeth might feel betrayed by Percy and their relationship would be severely strained. They would have a lot of emotional turmoil to work through. Meanwhile, the outside world would be in chaos. The gods might get involved, seeing as two of their powerful demigod children are in a strange situation. Percy would have to find a way to make things right, either by undoing what he did or by justifying his actions in some way.
Tony may develop a darker side. The allure of the Infinity Stones' power could corrupt him. He might start to make decisions that are not in the best interest of the world but rather for his own gain or to satisfy his newfound thirst for power. This would create a lot of conflict, both within himself and with his friends, and add a whole new dimension to the fanfiction.
In some fanfictions, Padme's kidnapping by Anakin could be the catalyst for Anakin's full - fledged turn to the dark side. His actions could isolate him further from the Jedi, and as he tries to hold on to Padme against her will, he might start to embrace more and more of the dark side's teachings, leading to a darker and more tragic story arc for both him and Padme.
Tony would likely be defiant. He's not the type to cower in the face of danger. He might immediately start looking for weaknesses in Thanos' setup and try to escape on his own terms.