Following his pursuit by Kirill (in The Bourne Supremacy), Jason Bourne (Matt Damon) evades Moscow police while wounded and deals with more flashbacks of when he first joined Operation Treadstone. Six weeks later, CIA Deputy Director Pamela Landy (Joan Allen) divulges the audiotaped confession of Ward Abbott, the late former head of Treadstone, to Director Ezra Kramer (Scott Glenn). Meanwhile, in Turin, journalist Simon Ross (Paddy Considine) of The Guardian meets an informant to learn about Bourne and Operation Blackbriar, the program succeeding Treadstone. The CIA tracks Ross as he returns to London, after his mention of "Blackbriar" during a cell phone call to his editor is detected by the ECHELON system. Bourne reappears in Paris to inform Martin Kreutz (Daniel Brühl), the brother of his girlfriend Marie Helena Kreutz (Franka Potente), of her assassination in India, also in the previous film.
Bourne reads Ross's articles and arranges a meeting with him at London Waterloo station. Bourne realizes that the CIA is following Ross and helps him evade capture for a while, but when he panics and ignores Bourne's instructions, Ross is shot and killed by Blackbriar assassin Paz (Édgar Ramírez), in the middle of a busy station, on orders of Deputy Director Noah Vosen (David Strathairn). Vosen's team, reluctantly assisted by Landy, analyzes Ross's notes and identifies his source as Neal Daniels (Colin Stinton), a CIA Station chief involved with Treadstone and Blackbriar. Bourne makes his way to Daniels' office in Madrid but finds it empty. He incapacitates gunmen sent by Vosen and Landy. Nicky Parsons (Julia Stiles), a former Treadstone operative who shares a history with Bourne, tells him that Daniels has fled to Tangier and aids his escape from an arriving CIA unit.