Ballard said Navy Secretary John Lehman knew of the plan.
"But the Navy never expected me to find the Titanic, and so when that happened, they got really nervous because of the publicity," Ballard said.
"But people were so focused on the legend of the Titanic they never connected the dots."
(Read about Ballard in National Geographic Magazine.)
The Thresher and Scorpion had sunk in the North Atlantic Ocean at depths of between 10,000 and 15,000 feet (3,000 and 4,600 meters).
The military wanted to know the fate of the nuclear reactors that powered the ships, Ballard said.
This knowledge was to help determine the environmental safety of disposing of additional nuclear materials in the oceans.
The Navy also wanted to find out if there was any evidence to support the theory that the Scorpion had been shot down by the Soviets.
Ballard's data showed that the nuclear reactors were safe on the ocean bottom and were having no impact on the environment, according to Thunman.
The data also confirmed that Thresher likely had sunk after a piping failure led to a nuclear power collapse, he added. Details surrounding the Scorpion are less certain.
A catastrophic mishap of some sort led to a flooding of the forward end of the submarine, Thunman said. The rear end remained sealed and imploded once the sub sank beneath a certain depth.
"We saw no indication of some sort of external weapon that caused the ship to go down," Thunman said—dismissing the theory that the Russians torpedoed the submarine in retaliation for spying.
While searching for the sunken submarines, Ballard learned an invaluable lesson on the effects of ocean currents on sinking debris: The heaviest stuff sinks quickly.
The result is a debris trail laid out according to the physics of the currents.
With just 12 days left over in his mission, Ballard began searching for the Titanic, using this information to track down the ocean liner. He speculated that the ship had broken in half and left a debris trail as it sank.
"That's what saved our butts," Ballard said. "It turned out to be true."
The explorer has since used a similar technique to find other sunken ships and treasures, including his recent expeditions to the Black Sea.
Are these expeditions also part of top-secret missions? After all, the Black Sea is in the volatile Middle East.
"The Cold War is over," Ballard said. "I'm no longer in the Navy."
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