I Believe In Peace (You've Gone Too Far)
Instead of betraying Tony and the accords, Natasha slightly stalls Steve and Bucky, allowing Peter to shoot a taser-web at Steve and then taking down Bucky with her Widow bites. As she hasn't gone against the accords she's in the clear, Rhodey doesn't have to chase a quinjet and therefore doesn't fall, and Tony watches over the Rogues' arrest and makes sure that they are contained but not oppressed, so someone tells him about Zemo, and he lets the appropriate agencies know so that they arrest him. They dig up Steve's lies (Natasha admits that she also knew but that she believed that it would be better if someone who hadn't betrayed him before told him, so when Steve said that he had told him and that was why he drew back so much she believed him) and Tony decides that now he could give the public his side about Ultron and Johannesburg as Wanda has proved to disregard anyone's well-being if they are in the way of what she wants. They find out her involvement and sentence her to life in a prison for the enhanced, they also find a magic user that can check for mind damage, finds extreme damage in Tony's mind and lesser damage in Clint's and Natasha's minds and heals them all. Tony remembers that he had a backup program to put back together JARVIS if he ever was damaged too much, and gets back his son. Vision decides that Wanda's disregard for him was not healthy so he seeks a therapist and gets help.
Years later all the Earth's enhanced have united in teams all over the world, so when Bruce comes to warn them about Thanos, they are ready and beat his purple butt without any casualties. Also, because she wasn't such a turncoat, Natasha becomes the cool aunt to Peter, Harley, MJ and Ned.