Unfortunately for U.S. prosecutors, none of (the evidence) actually made al-Arian a terrorist — PIJ’s North American leader, they insisted — which is why in 2005 a jury in Tampa, Fla., acquitted the former computer-engineering professor on eight charges and deadlocked on nine others. (Al-Arian’s defense also maintained that the prosecution’s case was based in part on a letter that was seized by the feds at al-Arian’s home but had never been sent.) It was one of the Bush Administration’s sharpest humiliations and a glaring example of its chronic overreach in post-9/11 terrorism cases. And critics say what happened next in the al-Arian case was just as bad, a classic illustration of how the Bush government’s ethical breaches, disdain for due process and perhaps anti-Muslim bias … (Read “When Terrorism Charges Just Won’t Stick.”)

More than three years after the conclusion of al-Arian’s trial, his legal saga drags on. After spending most of that time behind bars, he is now under house arrest at his daughter’s home in Virginia. But a U.S. district judge in Alexandria, Va., Leonie Brinkema, may be putting the brakes on al-Arian’s ordeal, and is questioning the Justice Department’s tactics in prolonging it. “I think there’s something more important here,” Brinkema said during a hearing last week, “and that’s the integrity of the Justice Department.”

Brinkema’s focus is the plea deal al-Arian signed in 2006 to avoid a retrial on the deadlocked terrorism charges. Under its terms, al-Arian, 51, a Kuwaiti-born Palestinian who since 1986 had been an instructor at the University of South Florida in Tampa, pleaded guilty to one count of conspiracy and was, after taking time already served into account, to be deported nearly immediately. But a federal prosecutor in Virginia evidently had no intention of allowing al-Arian to leave the country. Unbeknownst to defense lawyers at the time, Assistant U.S. Attorney Gordon Kromberg was preparing to subpoena al-Arian in a separate case. (Read “How the U.S. Lost a Terrorism Deal.”)

Instead of being sent back to the Middle East, al-Arian was called by Kromberg to testify before a grand jury looking into a Virginia-based Islamic think tank, the International Institute for Islamic Thought (IIIT). But because he believed Kromberg’s subpoena violated his plea agreement, al-Arian refused to cooperate. Last year, as a result, he was indicted for criminal contempt. All the while, despite his controversial history, his case has become a cause célèbre among civil rights activists, and he has staged at least two hunger strikes.

What defense lawyers say is particularly shocking is the revelation — contained in a court document filed by the government last week in response to the court’s request for evidence regarding plea negotiations — that the Tampa-based federal prosecutors who had negotiated the plea agreement were aware of Kromberg’s plans but never disclosed them. “Lawyers have the obligation to each other to reveal [that kind of information] before someone signs away his liberty,” al-Arian defense attorney Jonathan Turley said in last week’s hearing, “particularly after he was just acquitted on a number of counts before a jury.”

Kromberg also revealed last week for the first time that the prosecutors who had tried al-Arian in Florida did not want their Virginia colleagues to proceed with the subpoena but kept quiet about it anyway. One possible reason, say defense lawyers: had the defense team known that its client would be compelled to testify in a separate case, the plea deal might have crumbled, denying the Tampa prosecutors even that one conviction. The U.S. Attorney’s offices in Florida and Virginia would not comment when contacted by TIME, and the reasons for their actions in the case may never be officially disclosed, since federal prosecutors refuse to hand over to the court internal communications regarding the 2006 plea-deal negotiations and the Virginia subpoena.

Turley charged last week that prosecutors had “negotiated in bad faith,” adding, “It’s the type of behavior that doesn’t just shock the conscience of a court. It makes it impossible for defense attorneys and prosecutors to work.” Kromberg insisted there were no ethical lapses and said Florida prosecutors didn’t care “a whit” about what was going on in Virginia, which appeared to contradict his earlier statement that the Florida prosecutors didn’t want their Virginia colleagues to subpoena al-Arian. “There was no collaboration between Florida and Virginia,” he said. Besides, Kromberg noted that when the federal judge in the 2005 trial sentenced al-Arian on the one count to the maximum 57 months instead of the expected 46 (which, given time served, would have meant al-Arian’s almost immediate deportation), it kept al-Arian in the U.S. for an additional year and allowed the Virginia office to move ahead with its subpoena.

But Kromberg himself is also at issue in the case. A 16-year Justice Department veteran known for taking on high-profile terrorism cases, he’s been accused of making anti-Muslim slurs. A 2006 affidavit filed by Tampa attorney Jack Fernandez, who served on al-Arian’s defense team, alleges that Kromberg refused to delay a hearing scheduled to take place during the Muslim holiday of Ramadan. “If they can kill each other during Ramadan, they can appear before the grand jury,” Kromberg said, according to the affidavit. “All they can’t do is eat before sunset. I am not going to put off Dr. al-Arian’s grand jury appearance just to assist in what is becoming the Islamization of America.”

Kromberg has not commented publicly on the affidavit, and his office told TIME that neither he nor anyone else there would have anything to say on the matter; prosecutors have not yet said whether they’ll press ahead now on the criminal-contempt charges against al-Arian. Last week Brinkema gave the defense the go-ahead to file a motion to dismiss those charges. “I think there are significant questions about what actually happened,” she said. “The Justice Department is not a fishmonger.”