The Emergency Protocols detailed, among other things, the actions the British government was to take in the event of an alien incursion. They listed people who could help in such a crisis, notably the Doctor and members of UNIT.
When the Emergency Protocols had been invoked, military officials could authorise immediate executions. Computer software would search all communications for key words.
When a Slitheen craft landed in the River Thames and the Prime Minister went missing, the Emergency Protocols were handed to Joseph Green or more precisely, the Slitheen posing as him.
Jackie Tyler phoned the BBC's alien helpline and told them about the Doctor. The computer software detected this and the word "TARDIS", initiating a Code Nine. (TV: Aliens of London)
While hiding in the Cabinet Room of 10 Downing Street, Harriet Jones browsed the protocols for any information that could help them defeat the Slitheen. Most of the people it listed were already dead. (TV: World War Three)