The trial received significant attention from local media outlets. The four-week trial was conducted in Brooklyn's Federal court.
The defense alleged that Siraj was "entrapped" into plotting the crime, after incitement of hatred by the police informant. Using his hatred of America, they claimed, he was convinced to commit a crime against American civilians, which he would not normally have been inclined to do. Many jurors said in anonymous interviews after the case that the "entrapment defense" was the most convincing in their hesitation to convict him.
They attacked the credibility of the prosecution's lead witness, Osama Eldawoody, on grounds that he was paid a total of $100,000 for his work as an informer, $25,000 of which he received during the year he conversed with Siraj. It was the informant's salary, they argued, that kept him interested in the issue and encouraged him to bring Siraj into such a predicament. However, Eldawoody did not turn Siraj in for the pay, he said, but rather, as a good Muslim who believed that his faith was not one to be degraded into one of terrorism and violent activity. His compensation was for a tough job, he said, because he had to be circumspect in his demeanor to conceal his true identity. He is not likely to work for the NYPD again, simply because he may be recognized from the trial and/or his previous eavesdroppings.
The validity of the tapes was raised, and it was asserted that they may have been subject to review and censorship by the New York City Police Department, which was working alongside Eldawoody during his information-gathering visits. It was asserted that perhaps that the tapes were reviewed for incriminating content and may have been selectively edited—either by deletion or by Eldawoody himself—to leave out statements of encouragement and "entrapment" by Eldawoody that could have been critical proof for the defense.
The prosecutors, Todd Harrison and Marshall L. Miller, used digital recording from the defendant's conversations with Eldawoody, which were secretly made by the informant and handed to the police department as evidence. In these recordings, Siraj expressed excitement and pride in a plot to kill American civilians in Herald Square, which was strongly incriminating, albeit in a crime the defense felt was framed. The prosecution called their main witness, Eldawoody, who was the part-time police informant and a nuclear engineer used by the New York City's Police Department to infiltrate and eavesdrop on Islamic congregations around the city.
They attacked Siraj's credibility strongly because of many anti-American and anti-Semitic remarks he had made, some far before he had been encouraged into the bomb plot. These remarks, which would be regarded as reprehensible by the far majority of Americans, served to alienate the defendant as an ally to terrorist regimes and characterized him as a terrorist, despite the absence of weapons.
They were very convincing in showing that Siraj would have committed the crime if given the adequate weaponry. His sympathy of terrorist organizations such as Al-Qaeda and Hamas gave him a strikingly dangerous set of role models that would have meant he could have become violent and committed a terrorist act at any time if given the right amount of pressure. When Eldawoody told him that he was part of a terrorist organization from his country and that he could produce the materials to build a subway bomb, Siraj jumped onto the idea, they claim. They dismissed any allegations that Siraj was duped into the crime, stating that he was trying to "play dumb" rather than admit to his actual intentions. The fiery statements he made regarding the United States and his anti-American sentiment made him a dangerous individual at best. Eldawoody testified that "The defendant said that if anyone did... [a rape or murder] to his family, he would do the same thing, meaning a suicide bomb."
One of Siraj's friends testified against him as well. The individual, James Elshafay, was introduced to Eldawoody by Siraj and said he had every intention of carrying the act out if it had reached fruition. Elshafay, who is schizophrenic, was also a defendant in this case, but pleaded guilty to all charges and testified against his friend, leading the court to release him. Elshafay had actually stated that he was the intended bomber, while Siraj would be a lookout. According to Elshafay, Siraj did not want to bomb himself during the act, but he had talked with Elshafay and they had devised a plan where Elshafay would dress like a Hasidic Jew "'cause they know Jews aren't the ones doing it" and leave the bomb in a garbage can or under a bench, waiting to explode.
Siraj was encouraging of the terrorists, while claiming no allegiance to any group aside from the Islamic Thinkers Society and the Islamic Society of Bay Ridge. This has brought into question the nature of these groups as well, especially to the intelligence community, which has begun to bring these organizations into deeper investigation.
Eldawoody had many statements from Siraj that were : "The mission was not completed on 9/11," he quoted Siraj as saying, because "Wall Street was not attacked."
The jury reached a guilty verdict for all four charges brought against him, leading to four charges of bomb plotting and conspiracy. These convictions left out a major accusation, plotting to bomb a subway station, which could have led to a death sentence.
The defense's lead Defense Attorney, Martin Stolar, was disappointed and highly critical of the implications this case had for the civil rights of New Yorkers with these tactics being used by the NYPD. It represented the court precedent for a "police state" that gave the police license to instigate and eavesdrop on unfairly targeted people, especially Arab-Americans, he claimed. He rejected any statements that this guilty verdict was a success in the war on terrorism, saying "any claims that are made by the Police Department that they have made the citizens of the city of New York safer by convicting Shahawar Matin-- they have not."
This demonstrated a greater efficiency by the NYPD after 2001 in its counter-terrorism efforts. It had only about 20 officers working to combat terrorism before 9/11; since then, they now employ over a thousand. This has all been part of a protective measure led by Commissioner Ray Kelly to prevent future attacks in New York. The investigative measures also include new eavesdropping and infiltration tactics, which employ immigrants such as Eldawoody, originally from Egypt. They are able to interact with suspected terrorist individuals more easily and this case showed how convincing they may be when disguised. This has led to paranoia and distrust in the Islamic Society of Bay Ridge, which the defendant attended as well as mosques across New York City.
On January 8, 2007, a New York court sentenced Siraj to 30 years in prison.
A 2011 NPR report claimed some of the people associated with this group were imprisoned in a highly restrictive Communication Management Unit.