Baker joined the Criminal Division of the Department of Justice through the Attorney General's Honors Program in 1990 and went on to work as a federal prosecutor with the division's fraud section. In 1996 he joined Office of Intelligence Policy and Review. This government agency handles all Justice Department requests for surveillance authorizations under the terms of the 1978 Foreign Intelligence Surveillance Act, advises the Attorney General and all major intelligence-gathering agencies on legal issues relating to national security and surveillance, and "coordinates" the views of the intelligence community regarding intelligence legislation. Baker has often testified before Congress on behalf of Clinton and Bush administration intelligence policies, including defending The Patriot Act before the House Judiciary Committee. Regarding Baker's 2007 appearance on the PBSFrontline episode, "Spying on the Home Front", the show's producer, in a Washington Post online chat, referred to Baker as, "Mr. FISA himself". In 1998, Baker was promoted to deputy counsel for intelligence operations. From May 2001 he served as acting counsel, and in January 2002 was appointed counsel. In January 2014, he was appointed general counsel of the FBI. As of December 2017, newly appointed director Christopher A. Wray was reassigning him from this role with his new duties unclear.
Private sector
Baker's government service was interrupted twice by stints in the private sector. Baker was assistant general counsel for national security at Verizon Business from 2008 to 2009. He was associate general counsel with Bridgewater Associates, LP from 2012 to 2014.
Controversy
In 2004, according to The Washington Post, Baker was responsible for the discovery that "the government's failure to share information" regarding the NSA electronic surveillance program had "rendered useless a federal screening system" insisted upon by the United States Foreign Intelligence Surveillance Court to prevent "tainted information"—in U.S. case law, "fruit of the poisonous tree"—from being used before the court. Baker was reported to have informed presiding federal judgeColleen Kollar-Kotelly of the FISC, whose complaints to the Justice Department led to the temporary suspension of the NSA program. In 2007, according to The Washington Post, Baker revealed that he had informed Attorney General Alberto Gonzales "about mistakes the FBI has made or problems or violations or compliance incidents" prior to Gonzales' April 2005 testimony before the Senate Judiciary Committee that "here has not been one verified case of civil liberties abuse" after 2001. In 2017, Sinclair-owned Circa reported that Baker was under a Department of Justice criminal investigation for allegedly leaking classified national security information concerning the Trump administration to the media. The probe, described as "a strange interagency dispute that... attracted the attention of senior lawmakers", reportedly "ended with a decision not to charge anyone," per The Washington Post.
On May 10, 2019, Baker was interviewed for a taped Lawfare podcast, a justice-focused blog, during which he discussed his role in the FBI investigation of events during the 2016 presidential election that would be taken over by Robert S. Mueller III. Previously Baker had refrained from making public comment. He stated that he felt compelled to speak publicly now that the report is public and being characterized adversely by Trump and some members of his administration.
Views on encryption
Baker had long supported legislation requiring encryption systems to include a means to allow access by law enforcement with a proper warrant. Baker has argued that the cybersecurity threat has become so severe that law enforcement should embrace strong encryption and adapt to the lack of easy access to plaintext messages in a published essay and in a press interview.