Stu had an affair with Nina Fletcher. After Lynette found out about it, Nina fired him. Lynette then told Stu that he could go to Ed to get his job back, because Ed wouldn't want him to sue the whole company. Stu does just that. "Parcher & Murphy" is sued, and Ed fires a lot of employees, including Nina, and promotes Lynette to her position, making her his second-in-command. Before that, Lynette had asked Stu to play the role of a child kidnapper in order to teach her kids a lesson.
In the episode "Back in Business" Stu now works for Bree for the marketing of her cookbook. Lynette did not like the marketing plan Stu proposed and offered to replace it with one of hers. Bree refused, saying that she thought Stu's was better.