Within hours of being handed over to U.S. custody last week, a radical Islamic preacher from London named Abu Hamza al Masri was brought before a federal court in New York City. He got a seasoned criminal defense attorney, open hearings and is now in a federal lockup awaiting an August terror trial. It took days, not years.

Next week, the accused 9/11 mastermind Khalid Sheik Mohammed and four alleged accomplices get their second military commissions hearings of the Obama administration at the U.S. Navy base at Guantánamo. All five have been in U.S. custody for nine or more years.

The contrasts don’t end there.

One’s a military court. Another’s civilian. If the Sept. 11 prosecution ends in conviction and the military jury decides they deserve the death penalty, the secretary of defense will choose the method of execution. Masri and four other men who were extradited to U.S. custody from Britain can get at most life in prison, and release if they are acquitted.

From logistics to the law, the cases of Masri and Mohammed illustrate how encumbered the Guantánamo war court system has become.

Contrasting costs

• Subway vs. charter commercial airliner

The federal courthouse is a $2.25 subway ride away from the rest of New York City. Guantánamo lawyers, and everyone else from judge to victim family members, get to the Guantánamo proceedings on $90,000 charter jetliners. For the Oct. 15-19 proceedings, postponed from August by Tropical Storm Isaac, the Pentagon chartered two.

• Permanent offices vs. makeshift work space

Masri’s court-appointed defense lawyer, Jeremy Schneider, walked to his client’s arraignment from his downtown New York office, five blocks from the court. Guantánamo lawyers split their time between Washington Beltway offices and crude, cramped work space at Camp Justice, some of it recently declared a health hazard of toxic mold and rat droppings.

• Federal lockup vs. designer detention

Masri is held for trial next to the courthouse, in a 10-story federal lockup with solitary confinement for “high-risk” prisoners where lawyers can simply show up to see a client seven days a week. It costs $33,989 a year to keep an inmate in federal detention, according to the U.S. Bureau of Prisons. The Obama administration says it costs $800,000 a year to keep a prisoner at Guantánamo. To see a client, a defense lawyer needs to get a slot on the prison camp’s military roster and a ride on the $90,000 charter plane.

Different crimes

To be sure, the Sept. 11 attacks were a crime unparalleled in American history. Nearly 3,000 people were killed in the four hijackings, al-Qaida’s first attack on U.S. soil.

Masri, who was jailed in Britain since 2004 and convicted of incitement, is accused in U.S. federal court of abetting kidnappings of Americans in Yemen and conspiring to set up a terrorist training camp in Oregon, crimes that date back to the 1990s.

Each case took a roundabout route to U.S. justice. The same year Masri was convicted in a British court, the CIA moved Mohammed and his alleged co-conspirators to Guantánamo from years in secret agency detention specifically designed to keep them out of reach of the International Red Cross, as well as U.S. courts.

The Bush era Pentagon charged Mohammed with war crimes in 2008. But the Obama administration withdrew the case, and chose to try the case in New York City with a civilian judge and jury.