Season 6 sees a fresh start of Waterloo Road when dynamic Karen Fisher becomes the new Headmaster of this school, trying to bring positive changes. But she soon faces challenges when the Kirbys – sixth-former Jonah and 13-year-old genius Ruth enroll this school after home-studying and then many other issues. Besides, Karen also has to deal with her personal issues since her husband seems to have an affair and her daughter Bex disappears.