Mr. Kraft joined NASA’s predecessor agency in the 1940s as an engineer and became an omnipresent leader during the space agency’s heyday in the 1960s, a detail-oriented administrator who said he was “paralyzed with shock” on the day in 1961 when President John F. Kennedy declared the national priority of sending Americans to the moon by the end of the decade.

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Mr. Kraft played a crucial role in the achievements of John Glenn, Neil Armstrong and other space pioneers as a backstage visionary during the Mercury, Gemini and Apollo space missions. Mr. Kraft devised, implemented and managed NASA’s earliest efforts to usher astronauts into space and to bring them safely — if not always uneventfully — back to Earth.

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Long based at what is now the Johnson Space Center in Houston, Mr. Kraft provided an exacting and, at times, intimidating management style that proved exceptionally effective during the infancy of manned space flight. The United States was scrambling to catch up with the Soviet Union after the first Sputnik satellite launch in 1957 and after cosmonaut Yuri Gagarin became the first person to orbit Earth in 1961.

Much of Mr. Kraft’s legacy was cultural: He granted wonky, Earthbound number-crunchers power over celebrated astronauts and space agency chieftains.

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When Gemini 4 astronaut Ed White lingered during the first U.S. spacewalk in 1965, enjoying the scenery, Mr. Kraft commandeered the communications system and ordered him, “Get back in!” the ship.

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“This is the saddest day of my life,” White said, before heading back into the cockpit.

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The incident was indicative of the culture that Mr. Kraft set.

“It was, ‘I, the flight director, am in charge. Not you the astronaut, and not the head of NASA. You come to me,’ ” said author Michael Cassutt, who writes about the space program. “Much of the NASA culture as we envision it really derives from Chris Kraft.”

In the late 1950s and early 1960s, Mr. Kraft led the team that created Mission Control. He plunged into the minutiae, devising the first space flight plans, designing a communications and tracking system to monitor the astronauts and their health, and pondering what systems and signals they would need on board. He came to believe that most of the work of guiding humans in space would happen on Earth.

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His group set specific roles for ground controllers, deciding what tools they would use, what data they would see, whose conversations they would hear and how their seats would be arranged at Mission Control. Mr. Kraft also wrote rules to govern decision-making during missions.

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Mr. Kraft served as flight director for all six Mercury missions and several Gemini flights. He made the final call when American astronauts were “go” and shouldered the burden that even the smallest misstep might bring peril.

When Alan B. Shepard Jr. awaited launch in Freedom 7 in May 1961 — poised to become the first American to fly in space, a month after Gagarin’s triumph — Mr. Kraft began shaking so violently that he couldn’t see the microphone attached to his headset.

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“I leaned my hands on my console and forced myself to settle down. It was tough,” he recalled in his 2001 autobiography, “Flight: My Life in Mission Control.” “A man was sitting out there on top of a rocket . . . the potential for disaster was never more than a moment away.”

Mr. Kraft — often photographed wearing his communications headset or puffing on a celebratory cigar after a successful mission — became known for making authoritative decisions in crucial moments.

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He clashed with Mercury astronaut Scott Carpenter, the second American to orbit Earth, after his 1962 mission took a frightening turn when fuel ran low and a difficult reentry ended in a Caribbean splashdown 250 miles from the intended target.

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“He was completely ignoring our request to check his instruments,” Mr. Kraft wrote in his memoir. “I swore an oath that Scott Carpenter would never again fly in space. He didn’t.”

In 1967, Mr. Kraft listened at a communications console, helpless, when a deadly launchpad fire killed Apollo 1 astronauts Gus Grissom, White and Roger Chaffee. In the wake of the tragedy, Mr. Kraft and his team improved spacecraft design by fixing faulty wiring and allowing astronauts easier escape if needed, among other changes.

“When the fire happened, it was a mess. The hardware was bad. The planning was bad,” Mr. Kraft later told the Houston Chronicle. “It is a dastardly thing to talk about because it was the thing that ultimately saved the Apollo program. That is a terrible thing to say, but it’s true.”

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Barely a year later, Mr. Kraft helped persuade NASA leaders to attempt a daring moon orbit, ahead of schedule, for the Apollo 8 mission. Astronauts Frank Borman, Jim Lovell and Bill Anders would be the first to fly atop a powerful Saturn V rocket, the first to escape Earth’s gravity, the first to encounter and escape the moon’s gravity, and the first to see the dark side of the moon.

The mission proved wildly successful, with the crew orbiting the moon on Christmas Eve and reading from Genesis on a widely viewed television broadcast from space.

Mr. Kraft was in the control room when controllers he had trained eased Apollo 11’s Armstrong and Buzz Aldrin onto the surface of the moon on July 20, 1969, fulfilling Kennedy’s promise.

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The next year, when an oxygen tank exploded on Apollo 13 as it flew toward the moon, Mr. Kraft kept in close contact with flight director Gene Kranz, keeping tabs on Mission Control’s efforts to bring the hobbled spacecraft back to Earth and communicating with administrators and the public.

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Mr. Kraft objected to Hollywood’s depiction of the episode in the 1995 film “Apollo 13,” in which Kranz was portrayed by a vest-wearing Ed Harris.

“I was right there over Gene’s shoulder and he wasn’t nearly that dramatic,” Mr. Kraft told USA Today, adding in his memoir that the arguments in the film’s portrayal of Mission Control were “made up for good drama.”

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Kranz credited Mr. Kraft with providing invaluable leadership during the Apollo 13 crisis and beyond.

“He was the mentor, the teacher,” he said of Mr. Kraft in a 1999 NASA oral history. “Even though he physically left the console, he knew what these guys down here were doing. And he knew his job now was to give them the confidence to make the technical decisions . . . A spectacular man!”

In 2011, NASA renamed the center’s historic Mission Control building the Christopher C. Kraft Jr. Mission Control Center.

Roots of an explorer

Christopher Columbus Kraft Jr. was born in Phoebus, Va., now part of the city of Hampton, on Feb. 28, 1924. His German immigrant grandparents had bestowed the ocean-crossing explorer’s name on his father because he was born in New York City on the dedication day for Columbus Circle in 1892.

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Mr. Kraft’s father, a Veterans Administration finance officer, struggled with mental illness and was periodically hospitalized. Mr. Kraft’s mother worked as a nurse. They raised Chris Jr., their only child, in a house next to the town dump.

As a youngster, he sometimes got into fights but was also a high achiever who loved baseball and bugle corps. He enrolled at Virginia Tech in 1942. A childhood right-hand injury — he was accidentally burned in a fire — prevented him from enlisting in the Navy during World War II. He concentrated instead on baseball and on his studies in aeronautical engineering, a new discipline at the school.

After graduating in December 1944 on an accelerated wartime schedule, he went to work at the National Advisory Committee for Aeronautics (NACA) flight research division at Langley, Va., a few miles from his childhood home. NACA became NASA in 1958.

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In 1950, Mr. Kraft married Betty Anne Turnbull, his high school sweetheart. Beside his wife, survivors include two children.

Mr. Kraft retired from NASA in 1982 after a decade as director of the Johnson Space Center. He remained in Houston, working as a consultant for the industry and, in 1994 and 1995, leading a NASA review team that recommended handing space shuttle operations over to a private contractor.

In the latter part of his life, Mr. Kraft appeared in documentary films and offered public commentary on the space program. Speaking to NPR, he once quipped that he would not have ventured into space without being “anesthetized.” But he advocated for manned space flights long after the Apollo mission ended and when NASA seemed happy to focus innovation on robotic landers such as Pathfinder, which landed on Mars in 1997.

“Any argument for dropping or curtailing manned space flight is fallacious,” he wrote in his autobiography. “This nation can find no better investment in the health, safety, security, education, and overall well-being of the American public than for a visionary president to declare that Americans will land on Mars. And then make it happen.”