The Bourne Ultimatum
At the beginning of The Bourne Ultimatum, Simon Ross, a British investigative reporter working for the Guardian, is meeting with Neil Daniels in Turin, Italy to gather information for his next article. However, Daniels will only relinquish information regarding Blackbriar off the record and instructs Ross to turn off his tape recorder. After Ross returns to London, the ECHELON system detects Ross inquiring about Blackbriar with a colleague over his cell phone. This gains the immediate attention of the CIA, specifically the Blackbriar program. Noah Vosen arrives at the Blackbriar offices and takes command of their primary analyst team who immediately extract all known intelligence on Simon Ross in an attempt to trace his knowledge of Blackbriar back to its source. Vosen instructs the analysts to activate their asset in London, codenamed Paz and put him on standby. In the meantime, they continue to gather intelligence on Ross and work to tap his phone lines and hack his e-mails.
In the midst of their hunt, Jason Bourne contacts Ross on a colleague's work phone which confuses Vosen and the Blackbriar analysts. Bourne sets up a secret meeting with Ross at Waterloo Station in London, but unfortunately one of Blackbriar's agents is on-site and through audio surveillance intercepts Ross destination as he instructs a cabbie where to take him. Vosen sends their "grab" team to Waterloo in the hope of capturing Ross and renditioning him so they can interrogate him and learn who his source is. However, with Bourne's aid, Ross is able to evade his would-be captures for a time but is eventually overcome with anxiety and assassinated by Paz who was lying in wait with a Sig 552 Sniper, reminiscent of The Professor's from The Bourne Identity. Bourne manages to grab Ross' notes off of his person before fleeing the scene and pursuing Paz into the London Underground where Paz escaped on a tube train. The notes reveal Ross' source to be Daniels.
After the incident at Waterloo, CIA director Ezra Kramer orders Vosen to bring Pamela Landy on board due to her familiarity and prior experience with Bourne. It is through these circumstances that Landy asks Vosen about the true nature of Blackbriar. Vosen explains that Blackbriar is essentially the umbrella program for all of the CIA's black operations, including "lethal action" as Landy put it. One of the many pros in regards to Blackbriar is the ability for its commanders to make real-time decisions instead of waiting for authorization from Washington D.C.; "no more red tape" according to Vosen.
Landy is eventually forced into opposition against Vosen when he gives another asset, Desh Bouksani, the order to eliminate Nicky Parsons along with Bourne after he eliminates Daniels, which makes fairly good sense seeing how Nicky has now betrayed them for a rogue agent. Landy scolds Vosen that he doesn't have the authority to kill her, one of their own, which Vosen rebuts that he, in fact, does have the ability to kill a traitor. After Bourne eliminates Desh, he has Nicky use Desh's phone to code in that Bourne and Nicky had been successfully eliminated to throw Blackbriar off their trail. Bourne and Nicky part ways and Bourne heads to New York City to try to solve the puzzle of his origins.
When he arrives in New York he's aided by Landy and eventually tricks Vosen and his entire team into following her off-site while he infiltrates Vosen's office and manages to hack his safe to steal all of Vosen's classified documents containing Blackbriar's (and probably Treadstone's) secrets. When Bourne arrives at the training facility at 415 East 71st Street, he's met by Landy, to whom he gives the documents. She, in turn, faxes them off to a peer in Washington. Her actions ultimately lead to the arrest and prosecution of Vosen, Kramer and Dr. Albert Hirsch who was responsible for the design and implementation of the Treadstone/Blackbriar asset training program.
As the end of The Bourne Ultimatum, Blackbriar is for all intents and purposes shut down due to the criminal investigation.
In The Bourne Legacy, the cover-up for Blackbriar in the US Senate hearings contends that Blackbriar is the name of the operation to hunt down rogue Treadstone agent Jason Bourne. However, this is inconsistent with what Ward Abbott revealed to the Senate Oversight Committee about Blackbriar at the end of The Bourne Identity. The retcon for Blackbriar reveals that both it and Treadstone are both Beta programs for creating assassins with genetic engineering.