Note: the events in this movie take place at the same time during the events in the previous movie "The Bourne Ultimatum", thus making this movie a spin-off to the Bourne trilogy.
Aaron Cross (Jeremy Renner) is a member of Operation Outcome, one of the Department of Defense's black ops programs, which provides its agents with green pills that enhance physical abilities and blue pills that enhance mental abilities. He is given the moniker of "Number Five" and is deployed to Alaska for a training assignment, where he meets another Outcome operative, Number Three (Oscar Isaac). Their exchange is initially intense, as Number Three questions Cross as to why he is two days ahead of schedule for their rendezvous. Cross explains to him that he had to take a shortcut through a mountain ridge after having lost his kit of program essentials during his travels, including his requisite bloodwork he draws on schedule to send back to Outcome for analysis. This confounds Number Three, as the mountain ridge is generally acknowledged as being extremely difficult for agents to essay even when assisted with a program kit, yet Cross has done so in record time without one, a fact that ostensibly irritates Number Three, since it is implied that Cross has bested Number Three's unofficial "record". After a further exchange in which Number Three agrees to re-package send some of his bloodwork and label it Cross's, both men call an uneasy, implied truce to their tension. A fast-moving blizzard is on the horizon, and Number Three says Cross can stay an extra day, since he won't be able to get ahead of it, despite his early arrival. While lying in bed that evening, Cross happens to notice a number of carvings done in the woodwork above his head, including one of the name "Jason Bourne".
Meanwhile, Jason Bourne is in New York City exposing Operation Blackbriar and the Treadstone Project, leading to CIA Deputy Director Pamela Landy (Joan Allen) and Operation Blackbriar supervisor Noah Vosen (David Strathairn) being investigated by the FBI. Upon learning of this, CIA Director Ezra Kramer (Scott Glenn), also under investigation, calls Eric Byer (Edward Norton), a retired USAF Colonel responsible for overseeing the CIA's clandestine operations, for help.
In order to cover up the existence of the Blackbriar program, Byer decides to eliminate all Outcome assets and, upon discovering that both Numbers Three and Five are at the same location, deploys a U-CAV to terminate both agents. Cross's enhanced hearing picks up a faint echo in the distance, and Cross asks Number Three to confirm what he's just heard. He cannot, but he and Cross decide to split up and survey the area separately. Cross exits the cabin moments before the U-CAV missile deployed by Byer's people finds its target location and explodes, instantly killing Number Three. Cross uses a sniper rifle to destroy the U-CAV and, realizing that his superiors have ordered his assassination, goes about removing a tracking device that has been sewn into his abdomen, which he then forces a wolf that attacks him to swallow. Based on the active signal Cross's tracking device still emits, Byer realizes that Cross is still alive and orders a second U-CAV to be deployed to eliminate Cross once and for all. However, the missile keys on the tracking signal inside the wolf and destroys its target, allowing Byer to mistakenly assume that Cross has finally been terminated. He then sets his sights on terminating the remaining Outcome agents across the globe.
Byer issues a mandate to have agent handlers replace the other Outcome assets' green and blue pills with triangular yellow ones that will kill them in a matter of hours, and then goes about capturing one of Outcome's foremost scientists, Dr. Donald Foite (Zeljko Ivanek), chemically brainwashing him to shoot and kill his other colleagues, one-by-one in the Outcome research lab. The only survivor of the massacre is Dr. Marta Shearing (Rachel Weisz), who escapes after Foite commits suicide in order to avoid being questioned by security. Shearing is later attacked in her house by CIA agents ordered to kill her, but is rescued by Cross, who convinces her to help him after explaining who he is. Shearing reveals that Cross was genetically modified to retain the benefits of the green pills without need of continuous consumption, a process they call "viraling off". Because he hasn't taken a blue pill in several days, Cross realizes that he will soon lose his mental enhancement. He then coerces Shearing to travel to Manila with him, as the pills are manufactured there, in the hopes of being able to viral off the blue pills in the same manner he did the green.
On the way to Manila, Cross reveals to Shearing that he is actually Kenneth J. Kitsom, a U.S. Army soldier who was "killed" by a roadside bomb in the Iraq War and then offered an opportunity to serve his country via the Outcome program. Meanwhile, Byer continues to hunt down Shearing and discovers that she has been aided by Cross. From security intelligence gathered at major transportation hubs across the country, Byer deduces that Cross and Shearing have departed the US and are travelling to Manila, where the pills are manufactured, ostensibly to help Cross attempt to viral off the blue pills. Byers decides to activate Larx-03 (Louis Ozawa Changchien), the ultimate Outcome super soldier, who has had the viralling off process done for both the blue and green pills and has been programmed to become a completely lethal and emotionless killer. Larx-03 is deployed to Manila to eliminate Cross & Shearing while Cross is still presumably weak from the viraling off process. Byer also learns that Landy is expected to face charges for assisting Bourne, while Vosen is expected to be declared innocent and returned to duty.
In Manila, Cross and Shearing arrive at the factory where the pills are produced and Shearing administers to Cross the blue-pill viralling off procedure. Byer contacts the factory's supervisor and orders a lockdown, but Cross and Shearing are able to escape before Larx arrives and take shelter in a local apartment, where Shearing helps Cross through his recovery from the process, during which he hallucinates on his recruitment to Outcome, ironically achieved under Byer's direction. While partly delirious, he tells Shearing that he has money in his jacket and that if anything happens she should take it and get out of there. Cross also says that Shearing should go home, that she's done enough for him.
The following day, Larx-03 informs the local police of Cross' location while Shearing is away buying medicine. She is able to warn Cross, who has now fully recovered from the process, and he escapes from the police and rescues Shearing before they steal a motorcycle and escape, pursued by Larx. After a chase through the streets and marketplaces of Manila during which Cross is shot, Shearing kicks Larx-03 off from his motorcycle and into a pillar, killing him upon impact, while Cross' damaged motorcycle crashes alongside them as they come to rest. Cross and Shearing are then rescued by a boatman and bribe him with a stolen golden watch into taking them to a ferry, which they board, departing to places unknown.