Code Nine was a priority alarm initiated when computer software — activated on the release of the Emergency Protocols — detected important words.
When Jackie Tyler phoned the BBC alien helpline and told them about the Ninth Doctor and his TARDIS, the words were highlighted and a Code Nine was declared. Indra Ganesh informed General Asquith of this development. Ganesh did not realise that the General was really a Slitheen impersonating the General. (TV: Aliens of London)
Following the appearance of the Sycorax, Prime Minister Harriet Jones asked UNIT Major Blake if they had received a Code Nine, any sign of the Doctor. He replied that they had nothing yet. (TV: The Christmas Invasion)
At Torchwood Cardiff, Jack Harkness ordered Code Nine manoeuvres as his team engaged a partially converted Cyberman. (TV: Cyberwoman)