Soufan was called to Jordan in 1999 to investigate the Jordan Millennium Bombing plot, and discovered a box of documents delivered by Jordanian intelligence officials prior to the investigation, sitting on the floor of the CIA station, which contained maps showing the bomb sites. His find "embarrassed the CIA", according to a 2006 New Yorker profile of him.
In 2000, he was put in charge of the investigation of the USS Cole bombing. When given a transcript of the interrogations of Fahd Mohammed Ahmed al-Quso, he noticed a reference to a one-legged Afghan named "Khallad", whom he remembered as a source identified years earlier as Walid bin 'Attash; this helped the FBI to track down Abd al-Rahim al-Nashiri. Following the September 11th attacks, Soufan was one of eight FBI agents who spoke Arabic, and the only one in New York. Colleagues reported that he would sit on the floor with suspects, offer them tea and arguing over religion and politics in fluent Arabic, while drawing out information.
In 2005, Soufan approached Florida doctor Rafiq Abdus Sabir and pretended to be an Islamist militant, and asked him whether he would provide medical treatment to wounded fighters in the Iraq War.  When Sabir agreed to provide medical treatment, he was arrested and sentenced to 25 years' imprisonment for supporting terrorism.
Soufan obtained a confession from Salim Hamdan, accused of being a driver and bodyguard for Osama bin Laden. Soufan testified before his military tribunal that Hamdan was a hardened terrorist, with advance knowledge of the September 11th attacks.
He also obtained a confession from Ali al-Bahlul, an al Qaeda propagandist and Bin Laden media secretary accused of making a video celebrating the Cole attacks, and testified at his military tribunal as well.
On May 14, 2009 Soufan testified in front the Senate Judicial Committee for their hearing on torture. The hearing followed Obama's declassification of what is known as the "torture memos,"  and Soufan's testimony was essentially the same as an op-ed he authored for The New York Times on April 22, 2009 entitled "My Tortured Decision", which was published shortly after the memos were released.
Most notably, he claimed in his testimony that his interrogation of Abu Zubaydah had resulted in actionable intelligence, such as the identity of convicted terrorist José Padilla; and that thereafter, when waterboarding was performed on Abu Zubaydah, the flow of intelligence stopped. Soufan's statement is contrary to the ones made in the "torture memos," that were intent on making a legal case in favor of and justification for the use of these techniques.
Soufan re-stated this claim in a September 5, 2009, New York Times op-ed.
According to President George W. Bush's speechwriter Marc Thiessen, writing in the National Review in October 2009, both Soufan's testimony and his April 2009 New York Times op-ed are contradicted by CIA documents that state that Abu Zubaydah revealed the actionable intelligence only during the CIA's interrogation, which included rougher treatment than what the FBI had used.
- ↑ Giuliani G-Man Buys Manhattan Three-Bedroom Spread for $1.7 M., Max Abelson, New York Observer, January 29, 2008
- ↑ 2.0 2.1 2.2 Mayer, Jane, "The Dark Side: The Inside Story of How the War on Terror Turned Into a War on American Ideals", 2008. p. 191
- ↑ 3.0 3.1 3.2 Wright, Lawrence. The New Yorker, "The Agent", July 10, 2006
- ↑ New Yorker, Missed Opportunities, July 2006
- ↑ Wright, Lawrence, Looming Tower, (2006), p.364
- ↑ http://news.yahoo.com/s/ap/20070522/ap_on_re_us/terrorism_arrest
- ↑ http://nefafoundation.org/miscellaneous/FeaturedDocs/U.S._v_Sabir_DOJPR_Sent.pdf
- ↑ Template:Cite news mirror
- ↑ Template:Cite news
- ↑ Daily Times, Guantanamo Yemeni claims al-Qaeda's "best video", October 31, 2008
- ↑ C-SPAN videos of Ali Soufan senate testimony
- ↑  USDOJ: Office of Legal Counsel Memoranda
- ↑ What Torture Never Told Us, Ali Soufan, The New York Times, September 5, 2009
- ↑ New Documents Show the CIA, Not the FBI, Got Zubadayh to ‘Cough Up’ Jose Padilla, Marc Thiessen, National Review The Corner blog, October 31, 2009