MI5

MI5 was a branch of the British government's intelligence division.

20th century
Veronica Halliwell was the head of MI5 in 1997. She was ordered to shut down a publishing company which had released an exposé on UNIT. (NA: The Dying Days) The following year, Halliwell was assassinated by the Voracians. Her death was investigated by Harry Sullivan, now Deputy Director of the organisation. Hanson, the acting director, had been modified into a cyborg by the Voracians to serve as their agent. (MA: System Shock) In 1999, Harry Sullivan still remained in the organisation. (PDA: Millennium Shock)

21st century
In 2006, Margaret Blaine, whom the Slitheen killed and used as a bodysuit, was also a member of MI5. (DW: Aliens of London)

When the 456 contacted the British government again in September 2009, Floor 13 of Thames House, served as the location of a 456 Ambassador transported to Earth for negotiations. (TW: Children of Earth: Day Four) When Jack Harkness announced that Humanity would fight, the ambassador released a virus into the air of Thames House, now hermetically sealed electronically so that the virus could not escape. Many, if not all, of MI5 died on account of the virus. (TW: Children of Earth: Day Five)

Other information
MI5 knew of the plan to kidnap the American Envoy, though not that the Cybermen and Daleks had worked it out together (SP: Doctor Who: The Ultimate Adventure, BFA: The Ultimate Adventure)