Spooks returned for its fifth (10 part) series on 17 September 2006 with the first part of a two-part story, which saw elements in the British Government, MI6 and the UK press conspire in an attempt to over-throw the Parliament and the Prime Minister. These elements had agreed that for Britain to survive the threats posed by modern day terrorism, democracy had to be replaced with rule by committee in the 21st Century. Tactics used included the assassination of members of MI5, notably Colin, an attempt to kill the Home Secretary and kidnap the Prime Minister's son. The second part followed the next day (18 September), marking Spooks' return to BBC One's Monday night schedule.

Its storylines included a fake home-grown Al-Qaeda cell planning an attack on London (they are actually a Mossad team); the British government selling nuclear technology to Saudi Arabia; and the US administration selling arms to African dictators.

The series featured a more stable cast, more 2-part stories allowing for more complex plots and more dramatic use of split-screen. The ratings also remained consistent with those of the previous series, averaging 6 million viewers.

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