Miami ? Jose Padilla, the alleged al-Qaida operative held as an “enemy combatant” for more than three years, made his first appearance in court Thursday after he was taken from a Navy brig and flown to Miami.

The transfer from military to civilian custody began after a legal battle that went all the way to the Supreme Court.

Padilla appeared before a judge on criminal charges after he was taken from a brig in South Carolina and flown by military aircraft to Miami, said U.S. Marshals Service spokesman Dave Turner. He is to enter a plea today.

At the brief hearing, U.S. Magistrate Judge Barry Garber explained Padilla’s rights as a criminal defendant and asked whether he understood them.

“Yes, I do,” said Padilla, dressed in an orange prison jumpsuit and shackled at the wrists and ankles. He wore glasses and had a short haircut.

Garber set an afternoon hearing for today for Padilla to enter his plea and to determine whether he will remain in custody or be released on bail. Prosecutors said they would seek for him to be held before his trial.

Padilla, a former Chicago gang member, was arrested at Chicago’s O’Hare Airport in May 2002 and held by the Bush administration without criminal charges on suspicion of plotting to detonate a radioactive “dirty bomb” inside the United States.