A third series of again ten episodes was transmitted on BBC One in the autumn of 2004 and concluding 13 December. The first episode saw the introduction of Rupert Penry-Jones as Adam Carter, drafted in from MI6 to help investigate Tom's disappearance. He later took over Tom's position as Senior Case Officer as over the course of the series all three of the original leading trio (MacFadyen, Hawes, Oyelowo) left the programme, their departures staggered over the second, sixth, and tenth episodes respectively.

In episode six, Zoe is taken to court for misconduct during an operation and forced to leave MI5 and assume a new identity in Chile. She is replaced by Adam's wife Fiona (Olga Sosnovska).

The season garnered varied critical reactions, audience figures also dropping to a series average of 5.8 million viewers. Despite this the BBC commissioned a fourth series.