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The FBI first began surveilling Shafi after his father reported him missing while the family was vacationing in Egypt in August 2014. According to court records and FBI files, Shafi's father told U.S. Embassy officials that he was worried his son might have been "recruited" by "extreme imams." But he didn't mention any specific terrorist organizations.
What had actually happened, according to Shafi's attorneys and prosecutors in the case, is that Shafi and a friend, Abdul Niazi, flew to Turkey for two days to check on the Syrian refugee situation at the Istanbul airport. While there, Shafi handed out money and food before returning to Cairo. The government maintained it was a trial run that Shafi didn't go through with, while his attorneys maintained it was a humanitarian trip.
After Shafi returned to Cairo, his father wrote the embassy that all was resolved and requested that the government close any case it may have opened. In response, the FBI opened a full investigation. Two agents interviewed Shafi's parents upon their return to Fremont. Agents also interviewed Shafi and Niazi. The two young men maintained they went to Turkey to see the condition of refugees.
Then came an anonymous phone call to the FBI's Los Angeles field office. The caller claimed to be a friend of Yusuf Niazi, Abdul's older brother. Yusuf allegedly told the anonymous tipster in a phone conversation that his younger brother had tried to travel to Jordan to join ISIS. Yusuf, according to law enforcement records, had a criminal history and had been subjected to multiple restraining orders taken out by his father, whom Yusuf abused. He also was known to threaten violence against Abdul Niazi, so his motives in telling his friend that his younger brother and Shafi attempted to join ISIS were questionable.
Even so, JTTF agents hid near Shafi's house in Fremont and observed him exercising with his younger brothers in a park near his family's home. They described his exercise regimen as "paramilitary style" and surmised that he was training for combat after they saw him doing calisthenics and crawling on the ground. Shafi's lawyers say it was an innocent exercise routine and pointed out that boot camp-style workouts are very popular.
Meanwhile, sometime after Shafi's father reported him missing, the FBI obtained a Foreign Intelligence Surveillance Act warrant to intercept phone calls and search through text and email messages sent and received by Shafi. The warrant is a source of controversy because FISA was created by Congress to provide the FBI with a means of obtaining foreign intelligence that can't reasonably be obtained by normal investigative techniques. In other words, it wasn't meant to be used in criminal investigations involving U.S. citizens, such as in the case of Shafi and his friend Niazi, where, if law enforcement had probable cause to think a crime had been committed, or was about to be, it could have obtained a regular search warrant. FISA is a national security tool designed for use on non-U.S. citizens.
But the FBI used a FISA warrant to gather Shafi's communications. Later, the bureau obtained a standard criminal search warrant for Shafi's phone, computer, and email account. Contained in the intercepted communications was a conversation in which Shafi talked about wanting to join the Al-Nusra Front and live in Syria and condemning America as an "enemy," according to prosecutors.
Use of FISA to obtain some of this evidence makes defending his case difficult, say Shafi's attorneys. Neither he nor his counsel are allowed to view the warrant application and information contained in it, making it extremely difficult to challenge the admissibility of evidence obtained through it. They moved to have the FISA materials disclosed, but the government responded by obtaining a letter from U.S. Attorney Jeff Sessions stating that allowing Shafi and his attorneys just to see the warrant application would "harm the national security of the United States."
After reviewing the FISA materials without Shafi or his attorneys present, U.S. District Judge William Orrick, who oversees the case, decided in favor of the government. According to Orrick, the FBI had probable cause to believe Shafi was working as an agent of a foreign power when he traveled to Turkey, allegedly with the goal of entering Syria.
Complicating Shafi's case even further is his imprisonment under conditions his attorneys say constitute "solitary confinement." Prosecutors and Orrick call it "administrative segregation." Whatever the phrase for it, Shafi has been held alone, in a small cell in Oakland's Glenn Dyer Jail for approximately a year awaiting trial. He is allowed out of the cell for only one hour every two days and has very limited human contact. Orrick acknowledged in a hearing more than a year ago that administrative segregation is "not at first blush something that seems tenable for a very long period of time," but Alameda County officials say it's for Shafi's own safety. Assistant U.S. Attorney Candace Kelly told Orrick that Shafi's isolation was due to a possible threat overheard by a sheriff's deputy: "Not all prisoners are patriots."
Shafi's attorneys have also accused Alameda County sheriff's jail guards of illegally searching his cell and confiscating materials for his case, including notes that Shafi prepared for his attorneys regarding phone calls that were intercepted by the FBI using the FISA warrant. Sheriff's deputies then handed the materials over to FBI agents who provided copies to prosecutors in the case, according to court records.