At the the beginning of the film, she plays a crucial role in tracking down and finding Nicky Parsons after she hacked into to the CIA computer system to get information on all their Black Ops Programs before and after Jason Bourne. Heather Lee becomes focused on Jason Bourne after surveillance shows Nicky Parsons meeting Bourne in Greece. She does research in the CIA archives on Jason Bourne and concludes that he is still a patriot of the United States.
She then asks to be in charge of bringing Bourne back into the CIA. She is seen throughout the film to appear to help Bourne on several different occasions to gain his trust, however her intentions are uncertain towards the end of the film after she was secretly recorded by Bourne during her conversation with the CIA Deputy Director proposing killing Bourne if he does not want to come back into the Program.