Sami Al-Arian indictments and trial began on February 20, 2003, the U.S. Department of Justice announced that Sami Al-Arian had been arrested as the alleged leader of the Palestine Islamic Jihad (PIJ) in the U.S., and Secretary of the PIJ's central worldwide governing group (the "Shura Council"). It also charged three others living in the U.S., as well as four outside the U.S. These included Al-Arian's long-time top USF/WISE associate Ramadan Abdullah Shallah, who had been designated a Specially Designated Terrorist by the U.S. in 1995, and was accused of being Secretary General of the PIJ.

The PIJ was identified as an international terrorist organization, with cells throughout the world, that supports jihad and martyrdom, responsible for the deaths of among other Americans Alisa Flatow (20 years old) and Shoshana Ben-Yishai (16 years old). In 1995 the PIJ, Syrian-based and largely financed by Iran, had been designated a "Specially Designated Terrorist" by the U.S., and in 1997 it had been designated a "foreign terrorist organization".

A 50-count indictment returned by a federal grand jury in Tampa charged the defendants under the Racketeer Influenced and Corrupt Organizations Act (RICO) with operating a racketeering enterprise from 1984 that engaged in violent activities, as well as: conspiracy within the U.S. to kill and maim persons abroad, conspiracy to provide material support and resources to PIJ, conspiracy to violate emergency economic sanctions, engaging in various acts of interstate extortion, perjury, obstruction of justice, and immigration fraud. The indictment alleged a ten-year conspiracy to support PIJ worldwide, help solve internal PIJ disputes and financial problems, help disseminate PIJ claims it was responsible for terrorist attacks in Israel, and raise funds within the U.S. for "violent jihad." It alleged numerous PIJ-associated terrorist acts, resulting in the murders of over 100 people in Israel and the Occupied Territories. It claimed that PIJ, ICP, and WISE operated together as an illegal enterprise. It also alleged that the defendants used USF, where some of them were teachers or students, as cover and as a means to bring other PIJ members into the U.S., purportedly for academic meetings and conferences.

Attorney General John Ashcroft said that Al-Arian and his co-defendants played:

a substantial role in international terrorism. They are 'material supporters' of foreign terrorist organizations. They finance ... and assist acts of terror. Our message to them is clear: We make no distinction between those who carry out terrorist attacks, and those who knowingly finance, manage, or supervise terrorist organizations.

Al-Arian told reporters: "it's all about politics", and his attorney labeled the indictment a "work of fiction."

The indictment was later expanded into a 53-count superseding indictment in September 2004. It charged Al-Arian with: 1) conspiracy to commit racketeering; 2) conspiracy to murder or maim persons outside the U.S.; 3) conspiracy to provide material support to a foreign terrorist organization (the PIJ); 4) conspiracy to make and receive contributions of funds, goods, and services for the benefit of Specially Designated Terrorists (the PIJ); 5) use of the mail or any facility in interstate or foreign commerce to promote unlawful activity; 6) providing material support to a foreign terrorist organization; 7) money laundering; 8) attempt to procure naturalization unlawfully; and 9) obstruction of justice.

Trial

Al-Arian was tried with co-defendants Ghassan Ballut, Hatim Fariz, and Sameeh Hammoudeh in the United States District Court for the Middle District of Florida in Tampa, beginning on June 6, 2005. At trial, FBI agent Kerry Myers testified that the PIJ had planned an attack inside the U.S., but that all information about the plot was classified and he could not discuss it. Under cross-examination, Myers admitted that the PIJ had never carried out an attack outside Israel and the "occupied territories." Myers also testified that during its 10-year investigation of the defendants, the FBI intercepted 472,239 telephone calls on 18 tapped lines. However, none involved any discussion of an attack against the U.S. or reflected advance knowledge of attacks in the Middle East. Furthermore, some of the conversations occurred before PIJ was designated a Foreign Terrorist Organization in 1995.MegLaughlin, In his plea deal, what did Sami Al-Arian admit to?, St. Petersburg Times, April 23, 2006.

The five-month trial featured 80 witnesses and 400 transcripts of intercepted phone conversations and faxes. At the end of the prosecution's case, Al-Arian's attorneys rested without offering a defense, and the trial concluded on November 14, 2005. On December 6, 2005, after 13 days of deliberations, the jury acquitted Al-Arian on 8 of 17 counts. It deadlocked on the 9 other counts, with 10-2 favoring acquittal. The jury deadlocked on what the prosecutors described as three of the most important four conspiracy charges against Al-Arian, including the charge of conspiracy to provide services to the PIJ. A co-defendant also was acquitted on some charges and faced deadlocks on others, and two co-defendants were acquitted of all charges. U.S. Justice Department officials said they were considering whether to retry Al-Arian and co-defendant Hatem Fariz on the jury deadlock charges, one of which carried a life sentence.Meg Laughlin, Jennifer Liberto and Justin George, 8 times, Al-Arian hears 'Not guilty', St. Petersburg Times, December 7, 2005.

Jurors had mixed reactions. One who voted for acquittal said, "They have so little on [Al-Arian] that I'm disappointed. Most of us think he gave in because he was so sick of being in jail." But one of the jurors who believed Al-Arian was guilty on nine counts, causing a mistrial, said:

Like another person on the jury, I was convinced Mr. Al-Arian was still working with the PIJ after it was illegal. He was a very smart man and knew how not to be obvious. For me, the absence of evidence didn't mean there was no evidence. For me, it suggested a coverup, which he admitted to, in the plea agreement.

Guilty plea, pursuant to plea agreement

On February 28, 2006, Al-Arian signed a plea agreement in which he agreed to plead guilty to one count of conspiracy to contribute services to or for the benefit of the PIJ, a Specially Designated Terrorist organization, in violation of 18 U.S.C. § 371. In return, the U.S. Attorney: a) agreed to dismiss the other eight remaining charges in the superseding indictment; b) agreed not to charge Al-Arian with any other crimes known to the government at the time of the execution of the agreement; c) agreed not to enter any recommendation as to the imposition or amount of a fine; d) agreed with Al-Arian that an appropriate sentence would be 46–57 months in prison; and e) covenanted that if no adverse information were received suggesting such a recommendation to be unwarranted, the U.S. would recommend that Al-Arian receive a sentence "at the low end of the applicable guideline range, as calculated by the Court".

In the agreement, Al-Arian said that he was pleading guilty because he was "in fact" guilty. Al-Arian admitted knowing "that the PIJ achieved its objectives by, among other means, acts of violence."Elaine Silvestrini, "Al-Arian Admits His Role In Jihad" , Tampa Tribune, April 18, 2006 As part of the deal, Al-Arian agreed to be deported once his prison sentence ended.

The plea agreement provided that it was "limited to the Office of the United States Attorney for the Middle District of Florida and the Counterterrorism Section of the Department of Justice, and cannot bind other federal, state, or local prosecuting authorities." It also provided that it "constitutes the entire agreement between the government and [Al-Arian] ... and no other promises, agreements, or representations exist or have been made to [Al-Arian]".

Attorney General Alberto Gonzales said:

We have a responsibility not to allow our nation to become a safe haven for those who provide assistance to ... terrorists. Sami Al-Arian has already spent significant time behind bars, and will now lose the right to live in the country he calls home as a result of his confessed criminal conduct on behalf of the [PIJ], which is the same conduct he steadfastly denied in public statements over the past decade.

At the plea agreement hearing, U.S. Magistrate Thomas B. McCoun said, " if you're satisfied you're guilty or you believe it's in your best interest to plead guilty ... let me know that." Al-Arian replied, "I believe it's in my best interest to enter a plea."

The district court judge asked Al-Arian whether he had been promised anything else by anyone to induce his guilty plea, and he said that he had not. The plea agreement was unsealed and accepted by Judge James S. Moody on April 17, 2006. The count carried a maximum sentence of five years imprisonment, a $250,000 fine, and three years of supervised release. Al-Arian remained in custody pending his sentencing and deportation.

The deal came after 11 years of Federal Bureau of Investigation investigations, wiretaps and searches, and three and a half years of trial preparation, time Al-Arian spent in jail, most of it in solitary confinement.Meg Laughlin,Plea deal overcame the discord, St. Petersburg Times, April 24, 2006. Amnesty International said Al-Arian's pre-trial detention conditions "appeared to be 'gratuitously punitive'", and that "the restrictions imposed on Dr. Al-Arian appeared to go beyond what were necessary on security grounds and were inconsistent with international standards for humane treatment.".

Supporters of Al-Arian said the agreement was reached in part to end his family's suffering and to reunite them.Al-Arian gets 18 more months in prison, Associated Press, Published May 1, 2006Al-Arian's plea ends an ordeal; He agreed to a single count of conspiracy to end his family's turmoil, his attorney says., St. Petersburg Times, April 18, 2006.

On July 25, 2006, Fariz pleaded guilty to one count of providing nonviolent services to associates of Palestinian Islamic Jihad. He was sentenced to 37 months in prison. He was released on May 26, 2010.

Sentencing

Judge Moody sentenced al-Arian to the maximum 57 months in prison and three years of supervised release on May 1, 2006, and gave him credit for time served. Prosecutors said al-Arian would serve the balance of 19 months, and then be deported.

In his ruling, Moody harshly criticized al-Arian for doing nothing to stop suicide bombings perpetrated by the PIJ. "I find it interesting that you praise this country in public," he said, "the one you called Great Satan." He continued:

You lifted not one finger. To the contrary, you laughed when you heard of the bombings ... You are a master manipulator. The evidence is clear in this case. You were a leader of the PIJ."Ex-professor gets over 4 years in Florida Jihad case" , Reuters, May 1, 2006

Describing the PIJ suicide bombings, the judge said: "Anyone with even the slightest bit of human compassion would be sickened. Not you, you saw it as an opportunity to solicit more money to carry out more bombings." Reacting to Al-Arian's contention that he had raised money for charities, Moody said: "Your only connection to widows and orphans was that you create them."Stacy, Mitch, "Prof. Gets 18 Months More in Terror Case", The Washington Post, May 1, 2006, accessed March 8, 2010

Civil and criminal contempt prosecutions; 2006-2014