During the 2006–07 storyline "Civil War", which takes place in the aftermath of an explosion in a residential neighborhood in Stamford, Connecticut, and prompting calls for the government to register people with superhuman abilities, Sue's brother Johnny is beaten up by locals angered by his celebrity superhero status. Although Sue is initially part of the pro-registration side supporting the Superhuman Registration Act, she defects after the Thor clone, created by her husband Mister Fantastic and Tony Stark, kills Bill Foster. Sue leaves the Baxter Building, informing Reed via a note that their children are in his care, as she intends to join Captain America's underground resistance force. Her final injunction to her husband is a heartfelt request: "Please fix this."