According to a nine-count indictment, Muhanad Mahmoud Al Farekh, 30, helped prepare one of two explosive devices for use in the January 19, 2009 attack.
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Prosecutors said an accomplice detonated one device, while Al Farekh's fingerprints were found on packing tape for the second device, which a second accomplice carried and did not detonate. The military base was not identified.
Sean Maher, a court-appointed lawyer for Al Farekh, did not immediately respond to request for comment.
The Texas-born Al Farekh was charged with providing material support to al Qaeda, providing material support to terrorists and using explosives. He also faces six conspiracy counts including to murder Americans, use a weapon of mass destruction, bomb a government facility and aid Al qaeda.
Al Farekh faces up to life in prison if convicted. He is scheduled to be arraigned on Thursday before US District Judge Brian Cogan in Brooklyn, New York.
Also known as Abdullah al-Shami, Al Farekh had been detained in Pakistan prior to being flown to Brooklyn, where he first appeared last April 2.
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He pleaded not guilty on June 4 to three criminal counts in an indictment made public a week earlier.
Prosecutors accused Al Farekh of providing material support to al Qaeda from Dec. 2006 to Sept. 2009, in a plot that involved two fellow students from the University of Manitoba in Winnipeg, Canada.
Al Farekh was purportedly inspired by Anwar Al-Awlaki, a radical cleric whose teachings are believed by prosecutors to have inspired terrorism plots including the 2005 London subway bombings and a failed 2010 bombing in New York's Times Square.
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Al-Awlaki was killed in a 2011 US drone attack in Yemen.
The case is US v. Al Farekh, US District Court, Eastern District of New York, No. 15-cr-00268.
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