Fugitive in N.Y. Bombing Caught : Terrorism: Iraqi is nabbed in Pakistan and returned to U.S. after a 2-year manhunt. Ramzi Yousef is accused of masterminding the fatal 1993 trade center blast.

Ramzi Ahmed Yousef, the alleged mastermind of the 1993 World Trade Center bombing, was captured in Pakistan after a two-year international manhunt and spirited back here Wednesday under tight security to face charges in the massive explosion.

Officials said that Yousef, 27, an Iraqi national, was seized Tuesday. He is accused in the trade center blast that killed six people and injured more than 1,000--one of the worst acts of terrorism in the nation’s history.

Yousef is scheduled to be arraigned today before U.S. District Judge John Keenan in Manhattan.

In a statement, President Clinton called Yousef “one of the world’s most sought-after suspected terrorists” and noted that he was on the FBI’s most-wanted list.

“The arrest is a major step in the fight against terrorism,” the President said. “Terrorism will not pay. Terrorists will pay. We will continue to work with other nations to thwart those who would kill innocent citizens to further their own political aims.”

Pakistan’s interior minister, Nasirullah Babar, said Yousef arrived in Pakistan on Sunday, traveling with an Iraqi passport. He said that he did not know where Yousef had come from.

“He was under surveillance from the time he arrived,” Babar said.

He said that Yousef was arrested Tuesday at a hotel in Islamabad and immediately turned over to U.S. authorities for extradition.

Four of Yousef’s co-defendants were convicted last year of carrying out the trade center attack on Feb. 26, 1993, and were each sentenced to 240 years in prison. Yousef had been indicted with them on 11 counts in connection with the bombing.

As the investigation proceeded, it became clear that Yousef was a central figure. He had fled New York on the night of the blast using a false passport.

Government sources said Wednesday that Yousef’s activities before and after the bombing are under scrutiny, implying that further charges could be filed.

Sources said that Yousef was traced to Pakistan through an investigation in the Philippines last month when two men believed to be his accomplices were arrested as they were preparing bombs. Authorities said that the bombs were intended to be used against airlines.

Their seizures sparked a massive alert in the Far East, with increased security and hand searches of carry-on baggage on many U.S. flights.

Philippine officials relayed information to U.S. authorities that Yousef was believed to be involved in the bombing of a Philippine Airlines Boeing 747 in December in which one Japanese passenger was killed. But he escaped from the Philippines, where he had used the alias Abdul Basit Mahmood.

The scrutiny of Yousef and his accomplices came amid increased security in the Philippines and reports of plots to assassinate Pope John Paul II when he was there for a four-day visit last month.

Authorities who investigated the trade center tragedy determined that Yousef had helped plan and finance the bombing. During their inquiry, they were able to trace some of his movements in the United States. Traveling on an Iraqi passport, Yousef arrived at Kennedy International Airport on a Pakistani International Airlines plane from Karachi on Sept. 1, 1992. He had no visa but told immigration officials that he had bribed his way aboard the flight with a payment of $2,700.

Yousef said that he wanted to apply for political asylum--thus automatically invoking the right to a hearing.

His airline ticket was in the name of Azam Mohammed. He carried identification papers with his picture and the name Kharram Kahn. During the months just before entering the United States, he had traveled to Iraq and Jordan.

Arriving on the same flight from Karachi was Mohammad Ahmad Ajaj, a Jerusalem-born Palestinian who traveled under a false Swedish passport. Ajaj, who later was convicted in the trade center attack, was arrested at Kennedy Airport when he arrived, and authorities confiscated a dozen manuals that they said contained instructions for making bombs.

Laboratory tests made after the explosion showed that two of the manuals bore Yousef’s fingerprints. Other tests of a storage locker in Jersey City, N.J., where materials for the bomb were stored, also turned up Yousef’s fingerprints.

As the government case was revealed during the trade center trial, it became clear that Yousef was a shadowy but central figure. Robert E. Precht, the lawyer for Mohammed A. Salameh, one of the defendants, told jurors that his client had been “duped” by Yousef into purchasing bomb-making chemicals--for which Yousef had furnished the funds.

According to the testimony, Salameh rented the yellow van used to take the bomb into the trade center garage.

Officials said that Yousef planned his escape before the explosion. He convinced officials at Pakistan’s consulate here that he had misplaced his passport and, under the alias Abdul Basit, was given a new passport. Almost two weeks before the bombing, he booked a flight from New York to Pakistan.

Investigators later discovered that a month before the bombing, Salameh was injured in an automobile accident in Woodbridge, N.J. His companion in the car, Yousef, also was injured. In March, Yousef failed to appear for an immigration hearing as it became increasingly clear that he was a fugitive in the trade center bombing.

Last month, the FBI sent agents to the Philippines to investigate reports that Yousef had been arrested there. But fingerprints failed to match the two suspects who were in custody.

Police in Manila said, however, that Yousef apparently had escaped from police in January when they raided an apartment that he had occupied. Bomb-making equipment was recovered from the apartment, heightening concerns about the Pope’s visit.

Like the defendants convicted in the World Trade Center bombing, Yousef could face a maximum penalty of life in prison without possibility of parole. He will be arraigned in the same federal courthouse where Sheik Omar Abdel Rahman and 10 of his followers are on trial, charged with plotting a series of bombings in New York. The targets allegedly included the United Nations, two tunnels linking New York to New Jersey and the Manhattan headquarters of the FBI.

Prosecutors charge that the trade center bombing and the 1990 assassination of Rabbi Meir Kahane, founder of the militant Jewish Defense League, were essentially part of the same terrorist plot.

Earlier this week, Siddig Ibrahim Siddig Ali, the second most important defendant behind Abdel Rahman--who was the sheik’s translator and bodyguard--pleaded guilty to all charges and apparently has implicated all the other defendants. Siddig Ali said in open court during his plea that he had helped test the explosives used in the trade center bombing and helped trade center defendant Mohammed Abouhalima escape to Egypt. Abouhalima was subsequently captured by Egyptian authorities and returned to the United States. He was convicted in the earlier trial.

Yousef was believed to have received explosives training during the Afghan civil war. He was indicted in March, 1993. He in being detained in a federal prison near the courthouse in Manhattan’s Foley Square under heavy security. Authorities said that it is not clear whether a $2-million government reward for his arrest will be given to anyone.

FBI Director Louis J. Freeh credited the State Department and its diplomatic security service with the work that led to Yousef’s arrest.

Also convicted in the trade center bombing after a five-month trial was Nidal Ayyad, a chemical engineer who provided expertise in building the bomb, prosecutors said.

Goldman reported from New York and Ostrow from Washington. Times staff writer Robert L. Jackson contributed to this story from Washington.