The movie begins with Jason Bourne and Marie living in Goa, India under assumed identities. However, CIA officer Pamela Landy is investigating Bourne's past and starts to piece together his true identity. Meanwhile, Bourne is haunted by fragments of his past and begins to have nightmares about his former life as a trained assassin.
When the CIA attempts to purchase stolen Russian files, the operation is compromised by a Russian agent named Kirill, who kills the seller and a CIA contact. In retaliation, Bourne tracks Kirill to Moscow and kills him, but not before learning about an operation codenamed "Treadstone" that involved turning unwilling agents into assassins.
Back in the US, Landy discovers that Treadstone was responsible for creating Bourne and wants to bring him in for questioning. However, CIA Deputy Director Ward Abbott orders her to "clean up" the situation and eliminate Bourne.
Bourne meets with a former Treadstone technician named Nicky, who helps him track down Abbott. Bourne confronts Abbott and forces him to reveal that his real name is David Webb and that he joined Treadstone voluntarily after his wife and children were killed in a car accident.
In the final showdown, Landy confronts Abbott and admits that she now believes Bourne to be innocent. Bourne sneaks into Abbott's hotel room and kills him, before escaping and disappearing once again.
Overall, The Bourne Supremacy is a thrilling action film that explores issues of identity, memory and corruption within the intelligence community.