A TV breakthrough came when he appeared as Hareton Earnshaw in an adaptation of Wuthering Heights, screened on the ITV network in 1998. Further television drama work followed, including starring roles in the dramas Warriors (1999) and The Way We Live Now (2001), both for the BBC. Also in 2001, he earned acclaim for his starring role in the BBC Two drama serial Perfect Strangers, which was written and directed by Stephen Poliakoff. In 2002, he starred in The Project, a BBC drama charting New Labour's rise to power. He starred in Spooks, which became a success when screened on BBC One. A longer second season was screened in 2003, and a third season was broadcast in autumn 2004, with him leaving the series in the second episode. The series was aired as MI-5 on the A&E Network. In 2007 he appeared in the one-off Channel 4 drama Secret Life, which dealt with the controversial subject of paedophilia. Macfadyen won the 'Best Actor' award at the Royal Television Society 2007 Awards for this part, and was nominated for a BAFTA. He also appeared in a short Sketch for Comic Relief as the bridegroom in Mr. Bean's Wedding, alongside Rowan Atkinson and Michelle Ryan.