Richard Truly, a naval aviator and astronaut who flew aboard two early space shuttle missions and, as NASA’s associate administrator, guided the agency’s return to space after the Challenger disaster, died on Feb. 27 at his home in Genesee, Colo. He was 86.

The cause was atypical Parkinson’s disease, according to his wife, Colleen (Hanner) Truly.

Mr. Truly joined NASA in 1969, but he didn’t venture into space for 12 years, when he was the pilot of the shuttle program’s second orbital flight. The success of that flight proved that NASA could safely relaunch the Columbia shuttle, seven months after its maiden flight, and safely return it to earth.

The mission was supposed to last five days, but it was slashed to two after one of the Columbia’s fuel cells failed. (The Columbia disaster that killed a seven-person crew in 2003 occurred well after Mr. Truly had left NASA.)

In 1983, Mr. Truly, who was a captain at the time, commanded the Challenger during its third flight, the eighth overall in the shuttle program. It took off at night and landed in darkness — a first for the program. The flight also marked a personal distinction: Captain Truly was the first American grandfather in space.

Soon after, he retired from NASA to become the first commander of the Naval Space Command, which consolidated the Navy’s operations in space communications, navigation and surveillance.

But he returned to NASA as its associate administrator in charge of the shuttle program in 1986, less than a month after the Challenger broke apart 73 seconds into its flight due in part to launching in too cold temperatures, killing its seven-person crew, which included a teacher, Christa McAuliffe.

A month into his new job, Captain Truly said that the next shuttle would be launched only in daylight and in warm weather (the Challenger was launched at 36 degrees Fahrenheit), and that it would land in California instead of Cape Canaveral, Fla.

“I do not want you to think this conservative approach, this safe approach, which I think is the proper thing to do, is going to be a namby-pamby shuttle program,” he said. “The business of flying in space is a bold business.”

He added: “We cannot print enough money to make it totally risk-free. But we certainly are going to correct any mistakes we may have made in the past, and we are going to get it going again just as soon as we can under these guidelines.”

Captain Truly was also the chairman of the internal NASA task force that provided support to the presidential commission investigating the Challenger disaster. But his primary task was to return the shuttle program to flight.

“He was widely recognized as having done an excellent job in that responsibility,” John Logsdon, an emeritus professor at the Space Policy Institute at George Washington University, said in an email.

The job took 32 months: The launch of the Discovery on a four-day mission in late September 1988 lifted a long period of gloom and self-doubt for the agency.

“The nation,” Mr. Truly, who was by then a vice admiral, said at the time, “is going to have the shuttle as the backbone of its space program well into the next century.”

Richard Harrison Truly was born on Nov. 12, 1937, in Fayette, Miss. His father, James, was a lawyer for the Federal Trade Commission. His mother, Jessie Smith (Sheehan) Truly, was a teacher. They divorced when Richard was young.

Mr. Truly did not grow up wanting to be an aviator; rather, he recalled, he dreamed of driving a fire truck. “I never really intended to be a pilot,” he said in a NASA oral history in 2003. “It just never occurred to me that that would be a possibility.”

He studied engineering at the Georgia Institute of Technology on a Navy R.O.T.C. scholarship and became intrigued with aviation during two summers of Navy and Marine indoctrination. After graduating in 1959 with a bachelor’s degree in aeronautical engineering, he trained to be a naval aviator and was assigned to a fighter squadron.

Between 1960 and 1963, he made more than 300 landings, many of them at night, on the aircraft carriers Intrepid and Enterprise, then became a flight instructor.

In 1965, he was assigned to the Air Force’s Manned Orbiting Laboratory, a Cold War surveillance program that planned to send astronauts into orbit in a modified Gemini capsule connected to a cylindrical 50-foot-long laboratory. But the program was canceled in June 1969, and two months later, Mr. Truly was one of the seven astronauts from that program who joined NASA.

He worked in capsule communications for the manned Skylab and Apollo-Soyuz missions in the 1970s, after which he became a shuttle test pilot and the backup pilot for the first shuttle mission in 1981.

He left NASA shortly after his second shuttle mission when John F. Lehman Jr., the secretary of the Navy, asked him to take over the newly formed Naval Space Command in Dahlgren, Va. While there, he was promoted to vice admiral.

But after the Challenger tragedy, Mr. Lehman and the White House prevailed on him to return to NASA. He remembered walking to his office on his first day as associate administrator to find people crying in the corridor “because of the pounding they had been taking in the media,” he said in a 2012 interview with the Colorado School of Mines, where he was a trustee at the time.

“By that time,” he added, “rather than an airplane accident, it had been portrayed as NASA killed its crew. It was the start of the most tumultuous engineering, political, cultural, social endeavor that I ever found myself in.”

After three years as associate administrator, Admiral Truly was named administrator, the space agency’s top position, by President George H.W. Bush.

“This marks the first time in its distinguished history that NASA will be led by a hero of its own making, an astronaut who has been to space,” President Bush said at a news briefing.

But Admiral Truly’s three years atop NASA were difficult ones. The agency had problems with launch delays, shuttles leaking fuel and the discovery of a flawed mirror on the Hubble Space Telescope.

He was eventually forced to resign after clashing over the direction of NASA with Vice President Dan Quayle and his staff at the National Space Council, of which Mr. Quayle was the chairman.

Mr. Logsdon said that senior NASA employees, aerospace contractors and congressional overseers had offered positive assessments of Admiral Truly’s performance, but his tenure was viewed negatively by “those reformers who believed that NASA needed fundamental change and concluded that Truly was not the person to lead that change.”

After leaving NASA in February 1992, Admiral Truly served as the vice president and director of the Georgia Tech Research Institute, a nonprofit arm of Georgia Tech, and then as director of the Department of Energy’s National Renewable Energy Laboratory. He retired in 2005.

His honors included the Navy Distinguished Flying Cross, the Presidential Citizens Medal and two NASA Distinguished Service Medals.

In addition to his wife, he is survived by his daughter, Lee Rumbles; his sons, Mike and Dan; five grandchildren; and six great-grandchildren.

Admiral Truly admitted to being frightened at times when he faced danger and technical failure as a Navy pilot and an astronaut.

“Fear is a nice, healthy phenomenon,” he once said. “Any pilot who says he’s never been scared is lying.”

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