Two of the world's most sought after fugitives, the alleged al-Qaida leaders Khaled al-Sheikh Mohammed and Ramzi bin al-Shaibah, have boasted about how they planned the attacks on New York and Washington a year ago this week.

The two men, believed to be the chief of al-Qaida's military committee and the coordinator of the September 11 attacks respectively, spent two days last month with a senior journalist from al-Jazeera, the Arabic television station, at a hideaway in the Pakistani city of Karachi.

The contents of that interview, published in Spain's El Mundo newspaper yesterday, revealed not only that the target of the fourth hijacked airliner had been the Capitol in Washington - home to the US Senate and Congress - but also that al-Qaida was still functioning and operating from within Pakistan.

It also showed that two unnamed nuclear power stations were the original targets of the September 11 plot, known to its perpetrators as the Holy Tuesday Operation, but al-Qaida feared that such an attack "might get out of hand".

Yosri Fouda, the al-Jazeera journalist, revealed in El Mundo how a mystery caller invited him to Karachi last month to meet al-Qaida leaders and film a special report.

After two days in a run-down hotel, he was passed through a chain of people before being blindfolded, put in a car boot and driven to an apartment building. He was taken to a flat strewn with laptop computers and mobile phones and occupied by two men whom he recognised as the Yemeni Ramzi bin al-Shaibah and Khaled al-Sheikh Mohammed, thought to be a 38-year-old Kuwaiti. The US has offered a $25m reward for the pair.

"The two were proud of what they had organised. Al-Shaibah spoke with calm and authority. Mohammed was the man of action, al-Shaibah the theorist," Fouda said.

The first piece of the September 11 plot was put in place in 1992 when the Egyptian Mohammed Atta, who eventually led the attacks, was sent as a sleeper agent to Hamburg, Germany. There he studied urban planning, spending occasional periods in Afghanistan, the two men confirmed.

The idea came several years later from al-Qaida's military committee when it decided to refine a previously aborted plan - to fly airliners into 12 major American buildings - "in order to cause the greatest possible number of deaths and deal a huge blow to America on its own soil", according to Mohammed. "It was decided to abandon nuclear targets for the moment," Mohammed explained. "I mean for the moment," he added.

The operation took two and a half years to prepare. It was hatched and refined in a building known as the House of al-Gumad in the Afghan city of Kandahar, where Saudi al-Qaida fighters used to meet.

"We had a meeting attended by all four pilots including Nawaf Al Hazemi, Atta's right-hand man," al-Shaibah explained.

Al-Hazemi, who flew American Airlines Flight 77 into the Pentagon, has never before been identified as the operation's second in command. Atta was given operational control and chose the day for the attack.

Al-Shaibah, who failed to get a US visa to join the attackers, was in possession of a suitcase of souvenirs, including flight manuals and hand-written notes, from the Hamburg flat he shared with Atta. "He was an incredible man. May God place paradise at his feet so he can be, god willing, among the martyrs," said 30-year-old al-Shaibah.

Last spring the rest of the attack team, mainly Saudis, began training in Afghanistan. "They knew it was a martyr's operation, but they did not know details," explained Mohammed.

Atta and the pilots had started flying lessons in the US the previous year. Communication was by email, with targets given codenames. The Twin Towers were the "faculty of urban planning", the Pentagon was the "faculty of fine arts" and the Capitol was "the law faculty".

Ramzi kept on his laptop computer the last coded email sent to him by Atta, three weeks before the attacks, which spoke of the 19 attackers and the four targets.

"The first term starts in three weeks ... There are 19 certificates for private studies and four exams," the message read.

The exact date of the attack was given to al-Shaibah, using a numbers riddle, when Atta called him in Hamburg on August 29.

Al-Shaibah himself communicated the date, via messenger, to Osama bin Laden on September 6 after he had fled Hamburg for Pakistan.

Mohammed boasted that al-Qaida had a "department of martyrs" which was still active. "We have many volunteers," he said.

Fouda said his interviewees had demanded to hold on to his video recordings of them for two weeks so that they could cover their tracks. But the tapes were in fact never sent on to al-Jazeera.

"Khaled let his tongue run away by referring to Bin Laden in the past tense," wrote Fouda. "Something is not working well in the upper levels of al-Qaida. I used to think there was a 50% chance Bin Laden was alive, now I rather believe he is dead."

Fouda, however, said the two men he met seemed quite capable of taking over.

"Ramzi caused the greatest impression.He has the severe charisma, the vitality and the religious knowledge. This is our future Bin Laden."