Elizabeth II has been the Queen of England since 1952.
She was crowned queen in 1953, and the Wire planned to take the energy from the millions of Humans watching the coronation on their televisions. However, the Doctor foiled the Wire's plans. (DW: The Idiot's Lantern)
In 1988, her path almost crossed that of the Doctor at Windsor Castle. (DW: Silver Nemesis)
In 2001, Dr Who, an evil replica of the Doctor, repeatedly attempted to assassinate her, convinced she was the leader of an oppressive regime. During an appearance in Sheffield he eventually succeeded, but the self-doubts of his accomplice Jason, coupled with his own essentially fictional nature, meant that the Queen survived. (NA: Head Games)
The Doctor theorized that the royal family including Elizabeth II were Werewolves after Queen Victoria was attacked by one. (DW: Tooth and Claw)
