Jose Padilla will finally get his day in court.

After three years in custody, this American citizen, who was held as a enemy combatant, has been indicted on charges that he conspired to murder, kidnap and maim people overseas.

Padilla was arrested in Chicago and accused of planning a dirty bomb attack in this country. Since his detention at O’Hare International Airport, Padilla has been held in military custody and denied the basic rights afforded to all other citizens of this country.

He has been called a notorious terrorist who received training from al-Qaida and used as an example of why the president needs the authority to detain the country’s enemies in a system of extralegal, secret prisons.

Nowhere in the indictment are the original charges against Padilla. Although the charges he does face are serious and, if he’s convicted, could result in a life sentence, they don’t really compare to the original allegations. Evidence of those crimes, if there is any, is tainted by his long, illegal detention and the techniques used during questioning. Even if he were guilty, the way he has been treated by the government would likely preclude a successful prosecution.

The indictment ends an expected confrontation between the Bush administration and the Supreme Court about holding a U.S. citizen without formal charges and without access to a lawyer.

The conundrum the government faces illustrates the serious flaws of the country’s detention policies in the fight against al-Qaida and other terrorist organizations. By holding Padilla outside the law, it’s now impossible to seek justice for the original charges against him. If he had been planning a dirty bomb attack, he won’t be held accountable. If he hadn’t been, then he has been detained because the government made a mistake.

With his transfer into the federal justice system, Padilla will have the opportunity to hear the evidence against him, to challenge its veracity and seek a fair adjudication of his guilt. The federal courts have proven capable of handling such difficult cases.

The way Padilla has been treated has garbled U.S. law and set a dangerous double standard of justice that can be applied at the government’s whim.

In their appeal to the Supreme Court, Padilla’s lawyers asked, “Does the president have the power to seize American citizens in civilian settings on American soil and subject them to indefinite military detention without criminal charge or trial?”

The answer is no; it should have been no three years ago.