Harris played the main cast role of Thomas the Disciple, and later Thomas the Apostle in the 1999 biblical, historical, drama television film version of Jesus.His notable roles include that of Joy Division's lead singer Ian Curtis in Michael Winterbottom's 2002 film 24 Hour Party People and as Steven in the film short True Love (Once Removed), directed by Kevin Thomas. The film won Best Short Film at both the Palm Springs and Houston Film Festivals, was selected for the Clermont-Ferrand, London Raindance and Los Angeles Short Film festivals and also qualified for an Oscar nomination in 2004.
Harris also played Nick Sidney in the 2005 mockumentary Brothers of the Head, directed by Keith Fulton and Louis Pepe. In 2007, he appeared in his first feature film lead role as Eddie in Saxon, directed by Greg Loftin. In 2009, he played Stretch in Harry Brown, directed by Daniel Barber.
In 2010, Harris appeared in another film short, Native Son, written and directed by Scottish director Scott Graham. It premiered at the 2010 Cannes Film Festival.
In 2012, he played Fifield in Ridley Scott's Prometheus.
In 2014, Harris played Mick Santino in Deliver Us From Evil (2014), directed by Scott Derrickson and based upon the 2001 novel "Beware the Night" by Ralph Sarchie and Lisa Collier Cool. He was cast by Derrickson for the film, without an interview, based upon the director having seen the actor's performance in Harry Brown. That same year, he appeared as Gene Womack in Guy Myhill's The Goob. Myhill previously directed Harris in two film shorts, Two Halftimes to Hell (1997) and The Fabulous Bilsons (2001). Harris finished the year with his performances as Captain Sandy Browning in the critically acclaimed '71, directed by Yann Demange, for which he earned a British Independent Film Award nomination for Best Supporting Actor and as Campbell in Serena (2014), directed by Susanne Bier.
In 2015, Harris appeared as Solomon Lane in Mission: Impossible – Rogue Nation, directed by Christopher McQuarrie, and as Macduff in Justin Kurzel's Macbeth. His next project, Trespass Against Us, was released in 2016.
Harris filmed Possum in 2016, a film by Matthew Holness, in which he plays the main character. He reprised his role as Lane in the sequel Mission: Impossible – Fallout (2018).
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