WASHINGTON — Pete Rustan once devised a way to keep Air Force planes from being damaged by lightning. He led a project to build a spacecraft that performed important scientific experiments on the moon. He earned a PhD while serving as an Air Force intelligence officer. He became a designer of spy satellites.

All of those achievements came after he made a daring escape from Cuba to come to the United States.

Colonel Rustan retired from the Air Force in 1997 but went back to work after the terrorist attacks of Sept. 11, 2001, at a federal agency so secretive that its budget, projects, and accomplishments are classified information. His job was to lead research efforts in satellite reconnaissance for the military and CIA.

He might have been unknown to the general public, but Pedro L. ‘‘Pete’’ Rustan was something of a legend in the tight-lipped world of aerial intelligence and engineering. No one who worked with him is at liberty to say exactly what he did for a living.

Yet this much is true: When Colonel Rustan retired last August from the little-known National Reconnaissance Office, the Navy SEAL unit responsible for killing Osama bin Laden presented him with an American flag that flew at its forward operating base in Afghanistan.

On June 28, Colonel Rustan died at his home in Woodbridge, Va. He was 65 and had prostate cancer, said his wife, Alexandra Cary Rustan.

Any single element of Colonel Rustan’s life — political escapee, scientist, military officer, satellite designer — sounds like the stuff of fiction, but he embodied them all.

‘‘This guy was intense,’’ said Daniel S. Goldin, a former NASA administrator who knew Colonel Rustan for 20 years.

When Goldin took charge of NASA in 1992, one of his goals was to build spacecraft that could be deployed quickly and could produce important scientific results at relatively little cost. His slogan was ‘‘faster, better, cheaper.’’

Colonel Rustan managed a joint NASA-Defense Department project to build a 1,000-pound experimental spacecraft to go to the moon. The project, known as Clementine, took just 22 months from concept to launch pad.

‘‘Each time I went back,’’ Goldin said, ‘‘I gained more respect for him. He always seemed to take on things that were impossible.’’

Clementine went into space Jan. 25, 1994, and sent back 1.8 million images of the moon. It measured reflected light and radiation, created a topologic map of the lunar surface, and discovered evidence of frozen water in craters at the moon’s south pole.

After Clementine, Colonel Rustan went to work at the National Reconnaissance Office, which was created in 1961. Its existence was not officially made public until more than 30 years later.

All we know of Colonel Rustan’s work at the agency is that he helped design and manage spy satellites.

‘‘This is rocket science,’’ said Charlie Allen, a 47-year CIA veteran and former assistant director of the agency. ‘‘It has helped give the United States a decisive edge in the Cold War and in post-Cold War conflicts.’’

After Colonel Rustan retired from the Air Force, he consulted on commercial space ventures and for federal intelligence agencies. He was on an advisory board that recommended changes at the National Security Agency, one of the country’s largest intelligence agencies.

‘‘He was hands-down the most valuable member of that board,’’ said Michael V. Hayden, a former director of the National Security Agency and the CIA, in an interview. ‘‘He was creative. He was energetic. He was candid without ever being caustic or unkind.’’

After the 9/11 attacks, Colonel Rustan left the lucrative private sector and went back to work for the National Reconnaissance Office. He eventually led its Advanced Science Directorate and Mission Support Directorate.

In March, Colonel Rustan received the Philip J. Klass Lifetime Achievement Award from Aviation Week and Space Technology magazine. The citation said that, in the past decade, he designed two classified spacecraft that have ‘‘significantly improved US capabilities in intelligence, surveillance, and reconnaissance.’’

Even though his work was confidential, Colonel Rustan often traveled to theaters of war and was known to troops on the front lines, including members of SEAL Team 6, the elite commando unit that killed bin Laden on May 2, 2011.

Pedro Luis Rustan was born in 1946, in Guantanamo, Cuba, a small city about 40 miles from the US naval base at Guantanamo Bay. His father, a labor leader, was jailed as a political prisoner in 1961 by the regime of Fidel Castro.

In August 1967, when Pedro Rustan was 20 and a student at the University of Oriente-Santiago in Cuba, he looked up from his desk in the college library one evening to see his father standing before him. ‘‘This night we’re leaving,’’ said his father, who had escaped from prison through a ruse.

Colonel Rustan left his textbook open on the table and fled. With his father, two sisters, and a brother-in-law, he climbed inside a railroad boxcar carrying sugar cane. They jumped from the moving train as it approached the US naval base at Guantanamo and waded waist-deep through a snake-infested swamp before reaching a tall security fence topped with barbed wire. Colonel Rustan carried his younger sister on his back over the fence, then scaled a second fence inside the perimeter of the naval base. After they were picked up by US forces, the Rustans asked for political asylum.

In addition to his wife of 33 years, Colonel Rustan leaves two children, Peter of Bealeton, Va., and Amy Rustan of Washington; and three sisters.