A decade after exposing Operation Blackbriar and vanishing from the public eye, Jason Bourne (Matt Damon), born David Webb, finally overcomes his amnesia. He isolates himself from society, earning a living by participating in underground fighting rings. Meanwhile, Nicky Parsons (Julia Stiles), Bourne's former contact from Treadstone in Paris, has been working with a hacktivist group led by Christian Dassault and decides to infiltrate the CIA's mainframe to reveal their covert operations.
During her search, Parsons uncovers vital documents pertaining to Bourne's recruitment into the Treadstone program and his father's involvement, prompting her to travel to Athens to inform him. However, her breach of the CIA's system comes to the attention of Heather Lee (Alicia Vikander), head of CIA cyber ops, and Robert Dewey (Tommy Lee Jones), the powerful leader of the Iron Hand program, who intends to eliminate Bourne after the fallout from Blackbriar.
As Parsons and Bourne meet amidst a violent protest in Greece, they narrowly escape CIA operatives. She reveals that her hacking was for Dassault, who plans to leak all files on CIA black operations, and informs Bourne of the Iron Hand program, which poses an even greater threat than Treadstone. Tragedy strikes when Parsons is murdered by the Asset ([Vincent Cassel]), an assassin from the Blackbriar program with a vendetta against Bourne stemming from their tumultuous past.
Before her death, Parsons manages to pass Bourne the key to a locker containing crucial CIA files. Driven to uncover the truth about his history and family, Bourne tracks Dassault to Berlin, where he decrypts the files. He learns that his father, Richard Webb (Gregg Henry), was a CIA analyst involved in the inception of Treadstone. Unfortunately, the malware hidden in the files alerts the CIA to Bourne's whereabouts, leading Dewey to dispatch a team to apprehend him while Lee works to scrub the files to prevent further leaks.
The stakes escalate as Dassault confronts Bourne, mistakenly believing Bourne is deleting vital information. In a fierce struggle, Dassault meets his end. Seizing the moment, Lee reaches out to Bourne, hoping to persuade him to return to the agency. With the information gathered from Dassault's apartment, Bourne seeks out Malcolm Smith (Bill Camp), a former Treadstone operative, arranging a meeting in London.
As tensions rise, Lee convinces Dewey to allow her to personally approach Bourne for a potential reunion with the agency. However, unbeknownst to her, Dewey has secretly greenlit the Asset to eliminate both her and Bourne. Aware of the CIA's surveillance, Bourne skillfully eludes capture and confronts Smith, who reveals that Richard Webb intended to protect Bourne from recruitment. Tragically, the Asset kills Smith as Bourne escapes and reunites with Lee, who expresses her discontent with Dewey's ruthless methods and directs him to a tech convention in Las Vegas.
At this convention, Dewey is set to publicly debate Aaron Kalloor (Riz Ahmed), the socially-responsible CEO of Deep Dream, a company secretly funded by Dewey for mass surveillance purposes. Concerned about Kalloor's potential refusal to grant CIA access to his resources, Dewey authorizes the Asset to eliminate Kalloor and Lee.
Bourne arrives just in time to prevent the assassination and confronts Dewey, who tries to appeal to Bourne's sense of duty. In a fierce encounter, Bourne manages to eliminate Dewey's associate, while Lee kills Dewey in self-defense. Bourne then pursues the Asset, ultimately defeating him in a brutal climax.
In the aftermath, Lee gains the support of Edwin Russell (Scott Shepherd), Director of National Intelligence, advocating for a more humane CIA under her leadership. She proposes leveraging Bourne's trust to bring him back into the fold, while acknowledging the necessity of eliminating him if he declines. When she approaches Bourne with her proposition, he requests time to consider but discreetly leaves evidence of her intentions behind, revealing his lingering mistrust before vanishing once more into the shadows.
