His weapon? A super-secret 30,000-mile-long system of underwater microphones and cables planted on the ocean floor.
Since 1954, these electronic ears have eavesdropped on traffic in the Atlantic and Pacific Oceans and the Caribbean Sea.
Until recently, the intelligence "product" of hundreds of these undersea mikes was among the most carefully guarded of all military secrets.
"Sharing (with other governments) has been very selective and under specific agreement," said Dennis Conlon, chief oceanographer for the intelligence-gathering project.
Now the game has changed. This high-tech Cold War sword has turned plowshare, as sub-hunting is replaced by tracking whales and monitoring seismic activity.
The underwater sound surveillance system, or SOSUS, is capable of acoustically detecting and tracking submarines across wide expanses of ocean.
"I go after the sounds in the ocean: 'Acoustics R Us,' if you will," said the chisel-featured Gagnon, 41. "If you put a noise in the water, I hopefully will see or hear it."
For years, Gagnon tried to filter out the irrelevant noises made by whales, undersea volcanoes and non-threatening surface vessels.
"My ability to deal with submarines has improved dramatically because my understanding of seismic events and biologic entities is a lot better," Gagnon said. "The learning curve has been extremely steep over the past year."
For almost all of its clandestine life, however, SOSUS was the Navy's hole card in its tactical poker game with the Soviet Union.
The lid began to come off with the 1984 publication of ex-insurance man Tom Clancy's Hunt for Red October, which mentioned SOSUS (sound underwater) and described its sub-hunting ability.
Two years ago, the existence of the system, also known as Project Caesar, was partly declassified, but its capabilities remain top secret. The Navy is now debating whether and when to end all secrecy.
"In the event that a major threat returns, we don't want to leave ourselves vulnerable," said Cmdr. Dale Liechty, a Navy project director.
Estimates of the system's cost begin at $15 billion, though its current replacement cost would be far greater.
It consists of undersea cables connected to arrays of underwater microphones called hydrophones. A hydrophone converts the pressure pulses produced by sound into electronic signals that are fed by cable to a monitoring station on shore.
The biggest hydrophones are about the size of soda cans; the devices are grouped in multiples. The Navy isn't saying how many are in each array.
Water tends to slow the speed of sound, so it is ideal for picking up noise. The greater the number of hydrophones, the better listening capability - "sort of like having a bigger antenna or a larger eardrum," Conlon said.
Fixed arrays have been planted in the Atlantic and Pacific in roughly even numbers, Conlon said. There are also mobile hydrophone arrays, towed out to sea by ships, to allow for flexibility in sea-snooping. The towed arrays communicate through satellite relays. Together, the fixed and mobile arrays make up the Integrated Undersea Surveillance System.
A plan to add air-dropped arrays, code-named Ariadne, was killed in 1988.
To detect ever-quieter subs, the signal process had to be upgraded. Three generations of hydrophones have been installed, and cables have also evolved with the state of the art.
Still, the ability to track subs - or anything - comes down to the skill of the analyst.
"If the sub is out there and making sufficient noise, we will hear it," Liechty said. There are approximately 900 submarines in the world navies.
Oceanographer Gagnon is the leading expert among 200 analysts who read data at the main Atlantic listening post, the Naval Ocean Processing Facility in Dam Neck, Va., near Norfolk.
For about a year, the Navy has been sharing data with civilian scientists as part of a project called Whales '93. Amazed researchers have called the listening system "the acoustic Rosetta stone for whales."
And for deep-sea volcanoes, too. From December to July, SOSUS recorded 55,000 seismic events in the western Atlantic alone. Scientists in the previous 90 years had been able to document barely more than 100 undersea quakes.
Some of this analysis takes place at the Dual Use Analysis Center, a nondescript one-story building tucked in a corner of the Naval Research Facility, a bustling 60-acre base at the southern tip of the District of Columbia, across the Potomac River from National Airport.
Inside the center is a bank of four computers, each with its own speaker and nickname: Akula, which is Russian for shark; Skua, a seabird; Krill, the shrimp that whales feed on, and Monstro, for the leviathan in Pinocchio. Tapes of the sound data from the hydrophones are downloaded onto disks, which allows the data to be viewed as images, called spectrograms, and played over the loudspeakers.
A spectrogram is essentially what geophysicist Clyde Nishimura calls "a specialized piece of sheet music," a visual representation of the sounds.
Nishimura noted the dark blotches on the spectrogram, which he compared to musical notes. He and other analysts "read" these sounds to create a census of whales and other denizens of the deep.
Each sound, whether biological, geological or mechanical, produces a certain "signature" that can be read on the spectrogram. Operators are skilled at distinguishing mechanical sounds like those made by subs from biological sounds, such as those made by whales.
Gagnon compared the analysis to reading an image from the static of a TV screen. The sound produced by a hatch cover being opened on a submarine has a specific configuration. So, too, does a blue whale's call, which looks like a dark comma.
Before the Whales '93 program, submarine hunters were annoyed by the need to probe amid the "clutter" - noise made by marine mammals and volcanoes. Now the clutter is a new, rich source of information.
The transition was not completed without some skepticism from analysts such as Gagnon.
"At first, I chuckled about it," Gagnon said. "But I'm a good sailor and I was told to track whales, so I said aye, aye, sir.
"I had no idea of the amount of noise generated by whales," he said. ''All of a sudden, I could see hundreds of them out there."
Earlier this year, Gagnon tracked one of the approximately 1,000 blue whales in the Atlantic for 43 days over 1,450 miles.
Could he do the same with subs, which are much more quiet? Gagnon isn't saying.
For fans of old sub-hunting movies such as Run Silent, Run Deep, the question is: Can you recognize a particular sub and its captain?
"I'm pretty good, but I can't do it," Gagnon said. "I don't have to. I'm a medic, not a surgeon. My job is to kill subs."
Was, Gagnon should have said. The Navy is drastically downsizing the submarine surveillance program, and looking instead for commercial applications for the data, like Whales '93.
Once there were 26 worldwide listening posts. Now there are but seven, including Dam Neck and its Pacific equivalent at Ford Island in Hawaii.
As listening posts have dwindled, the hydrophone arrays have been turned off. Plans are to halve the surveillance system's 2,500 employees, about 1,100 of whom are analysts. Some of the system will be mothballed. The plan, according to Conlon, is to stop looking at the data.
Yet other people, such as oceanographers, dearly want this information. Soon it may be had, for a price.
The government is also experimenting with using the system to monitor the activity of other vessels, such as illegal drift-net fishing boats.
There is a reluctance, of course, to shut the thing down, given what a valuable tool it was when the Cold War meant Red Octobers, not blue whales.
Then, too, scientists are discovering there are sounds out there they still cannot recognize.
Beginning in March 1992, the hydrophones recorded a steady grinding noise in the South Pacific, which went on for months, stopped for a time, and then resumed.
"At first they thought it was drilling or some sort of seismic activity," Nishimura said, "but both have been ruled out.
Biologists theorized that it was some humongous blue whale, but nobody is certain.
Said Nishimura: "It's still an absolute mystery."