On Aug. 12, 2003, a Gulfstream IV aircraft carrying six passengers took off from Dulles International Airport and flew to Bangkok with fueling stops in Cold Bay, Alaska, and Osaka, Japan.

Before it returned four days later, the plane also touched down in Afghanistan, Sri Lanka, the United Arab Emirates and Ireland. As these unusual flights happened, U.S. officials took custody of an Indonesian terrorist, Riduan Isamuddin, who had been captured in Thailand and would spend the next three years being shuttled among secret prisons operated by the CIA.

The Gulfstream IV’s itinerary, as well as the $339,228.05 price tag for the journey, are among the details of shadowy CIA flights that have emerged in a small Upstate New York courthouse in a billing dispute between contractors. The court documents offer a rare glimpse of the costs and operations of the controversial rendition program.

For all the secrecy that once surrounded the CIA program, a significant part of its operation was entrusted to very small aviation companies whose previous experience involved flying sports teams across the country.

The August 2003 flights — and dozens of others to locations such as Bucharest, Romania; Baku, Azerbaijan; Cairo; Djibouti; Islamabad, Pakistan; and Tripoli, Libya — were organized by Sportsflight, a one-man aircraft brokerage business on Long Island. It secured a plane from Richmor Aviation, based near the Columbia County Airport in Hudson, N.Y. Richmor eventually sued Sportsflight for breach of contract. In the process, the costs and itineraries of numerous CIA flights became part of the court record.

In other cases, the government has invoked the “state secrets” privilege to shut down litigation over the CIA program, but the case in Columbia County proceeded uninterrupted in an almost empty courtroom. There were only two witnesses at the bench trial: Richmor President Mahlon Richards and Sportsflight owner Donald Moss.

In a 2009 judgment, largely upheld on appeal this year, Judge Paul Czajka awarded Richmor more than $1 million.

“I kept waiting for [the government] to contact me. I kept thinking, ‘Isn’t someone going to come up here and talk to me?’ ” said William F. Ryan, the attorney for Richmor, which manages and books charter flights for aircraft owned by others, and operates from a handful of small airports in New York, Connecticut and D.C. “No one ever did.”

Moss’s attorney, Jeffrey Heller, also said he was never contacted by any government official.

The more than 1,500 pages from the trial and appeals court files appear to include sensitive material, such as logs of air-to-ground phone calls made from the plane. These logs show multiple calls to CIA headquarters; to the cell- and home phones of a senior CIA official involved in the rendition program; and to a government contractor, Falls Church-based DynCorp, that worked for the CIA.

Attorneys for a London-based legal charity, Reprieve, which has been investigating the CIA program, discovered the Columbia County case and brought the court records to the attention of The Washington Post, the Associated Press and a British newspaper, the Guardian.

“This new evidence tells a chilling story, from the CIA’s efforts to disguise its illegal activities to the price it paid to ferry prisoners to torture chambers across the world,” said Cori Crider, Reprieve’s legal director. “If we are to avoid repeating our mistakes, we must have a full accounting of how this system was allowed to flourish under our very noses.”

The CIA declined to discuss the case. “The CIA does not, as a rule, comment on litigation, especially that to which we are not a party,” said spokeswoman Marie E. Harf.

Hunting terrorism suspects

In the wake of the Sept. 11, 2001, attacks, the CIA’s Rendition Group, a division of the agency’s CounterTerrorism Center, was tasked with finding terrorism suspects, orchestrating their capture and transferring them for interrogation to covert prison sites in allied countries.

The program was exposed by journalists, human rights activists and aviation enthusiasts who examined public flight records, identified the tail numbers of private planes suspected to be involved in rendition operations and then continued to spot those planes. President Obama closed the CIA’s secret interrogation program, but the administration continues to allow rendition in certain circumstances.

The Richmor plane — tail number N85VM — was identified publicly in 2005 after it was used in the rendition of Abu Omar, a Muslim cleric who was snatched off the streets of Milan and flown to Egypt. The company was managing the plane for its owner, Phillip Morse, vice chairman of Fenway Sports Group, parent company of the Boston Red Sox.

Richmor changed the tail number of the Gulfstream and complained in a letter to Sportsflight that it became the subject of “negative publicity, hate mail and the loss of a management customer as a consequence of the association of the N85VM with rendition flights.” The letter also stated that Richmor crews were not comfortable leaving the country and that the owners “are afraid to fly in their own aircraft.”

The CIA captured and rendered at least 100 terrorism suspects to other countries, including all of the high-value detainees currently held at Guantanamo Bay, Cuba. Among them was Isamuddin, better known as Hambali. He and the al-Qaeda-affiliated group he led are accused in the 2002 nightclub bombing in Bali, Indonesia.

The CIA used a network of at least 26 private planes that were leased through front companies and legitimate contractors. By 2007, the Council of Europe, which advocates for human rights and democracy, was able to identify 1,245 flights operated by the CIA that had passed through Europe; invoices in the Columbia County courthouse show numerous stops in Britain and Ireland.

The contracts for these and other flights had remained classified. Over 36 months, between 2002 and 2005, the Richmor plane flew at least 1,258 hours for the CIA, including routine flights to transfer personnel to Guantanamo Bay and other destinations, according to the court records.

The records include a contract stipulating that all flight crew members must be American-born citizens, not naturalized citizens or holders of green cards.

Richmor billed at a rate of $4,900 an hour for the use of the plane and earned at least $6 million over three years, according to the invoices and other court records. Richmor accounted for only a small percentage of the CIA’s business, according to publicly available records. That suggests that the agency paid tens of millions of dollars to use private planes in the aftermath of the Sept. 11 attacks to transport detainees and its own personnel.

‘A highly unusual situation’

In early 2002, DynCorp hired Sportsflight on behalf of the government to secure a plane with 10 seats and a range of nine hours for chartered flights. Sportsflight, in turn, guaranteed Richmor 50 hours of flight time a month, and it agreed to have a plane and crew on 12-hour standby.

Moss said he had an understanding with DynCorp that the company would not be required to provide passenger manifests. “This was a highly unusual situation,” he said. “But I received the waivers.”

At first, the subcontractors thought they were working for the State Department, which gave Richmor official letters saying it was providing “global support to U.S. embassies worldwide.” The letters also authorized Richmor to deviate from stated flight plans.

One letter is dated March 1, 2003, the date of the capture of Khalid Sheik Mohammed, the self-proclaimed mastermind of the Sept. 11 attacks. That suggests that the Richmor plane was used to transport him out of Pakistan, but there is no invoice for the relevant flight in the court record.

Ryan, Richmor’s attorney, said the company president became aware of what the planes were being used for shortly after the flights began.

“It was obvious,” he said. “They flew to Guantanamo and Germany and the Middle East with regularity.”

Or, as Richards put it while on the stand: “We were transporting government personnel and their invitees.”