An American terrorist suspect arrested five years ago and held without charge as an “enemy combatant” will finally go on trial today, but prosecutors have been forced to drop allegations of a radioactive bomb plot.

Jose Padilla became a cause célèbre for the US civil rights movement who argued he was held illegally after his arrest at Chicago’s O’Hare airport in 2002. He was accused of planning a dirty bomb attack on America.

Despite being a US citizen, he was classed as an “enemy combatant” and taken to a Navy base in South Carolina for interrogation. He was given no access to a lawyer and charged with no offences for three and a half years. He also claims he was tortured while in custody.

Mr Padilla will appear at a federal court in Miami today accused of plotting to murder, kidnap and maim people outside of the United States and of aiding a US al-Qaeda cell, which provided recruits and funding to Islamist extremists around the world.

The charges brought against Mr Padilla will be an embarrassment to the Justice Department who justified his extra-legal detention by citing far more serious allegations.

“The crimes he has been charged with pale in comparison to the initial allegations,” said Stephen Vladeck, a law professor University of Miami. “This is a far cry from being a major front in the government’s war on terrorism.”

The 36-year-old of Puerto Rican descent was a Chicago gang member before converting to Islam. He was arrested after returning from Pakistan where it is alleged he was undergoing jihadist training.

Adham Amin Hassoun and Kifah Wael Jayyousi, both 45, are also due in court today. They will also be charged with assisting an American al-Qaeda cell, it will be argued that they were the men responsible for recruiting Mr Padilla.

Mr Hassoun and Mr Jayyousi were under FBI surveillance for much longer than Mr Padilla. The prosecution will present hundreds of intercepted phone calls and various money transfers between the two men and alleged al-Qaeda operatives.

The key piece of evidence against Mr Padilla is an application form for an al-Qaeda training camp in Afghanistan, prosecutors say the document was filled in in July 2000 and bears his fingerprints.

There will be absolutely no mention of the dirty bomb plot, which led to his initial arrest, during the trial. Nothing Mr Padilla told interrogators during his three years in the military prison is admissible.

Mr Padilla was transferred to the civilian judicial system in 2005 before the Supreme Court was asked to rule on the legitimacy of his detention. In 2003 a panel of three judges ruled that the internment of a US citizen in a military camp outside the American legal system was not justified.

President Bush and the White House rejected this decision and relented only when a legal challenge in the Supreme Court was pending.

The then attorney-general, John Ashcroft, released details of the allegations against Mr Padilla. There were two major allegations. He was accused of conspiring with another man to blow up high-rise apartments in New York or Washington by renting as many flats as possible in a single block and leaking gas into them.

He was then said to have decided it would be impossible to rent so many apartments without raising suspicions. At this point he allegedly proposed the dirty bomb plot as an alternative.

The Justice Department billed his arrest as a major breakthrough in the War on Terror at a time when the intelligence services were under scrutiny for their investigations in the run up to the September 11 attacks.

Mr Padilla’s lawyers have alleged that he was subjected to sleep deprivation, threats of execution, exposure to noxious fumes and extreme heat and cold, and was forced to wear a hood during his detention at the Navy base.

In the case, which is expected to last until August, the three men will plead not guilty and could be sentenced to life imprisonment if found guilty.

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