Clarke then spent a further 3 years as a Commander, heading the Protection Command between 1997 and 2000, a role which placed him in charge of Royalty protection at the time of the death of Diana, Princess of Wales, followed by 2 years as deputy director of personnel from 2000 to 2002. In June 2002, Clarke became head of the Anti-terrorist Branch, later merged with Special Branch to form the Counter Terrorist Command, a role which put him in direct control of the investigation into the 7 July attacks on London and the failed bomb attempts of 21 July 2005.