The Navy’s reputation as a fearsome fighter is more than earned — on the high seas and in U.S. courts.

In the 75 years since the Navy started conducting war games in a vast expanse of the Pacific Ocean between the Hawaiian and California coasts, conservationists have often sought to restrict its use of bombs and sonar that harms marine mammals. Each time, the military branch blew the activists away, arguing that what’s good for the Navy is best for America.

That’s why a recent court loss, and the Navy’s surprise capitulation to working out a settlement agreement with conservation groups that was announced this week, is startling. For the activists, it was a win by a hopeless underdog, a mouse chasing an elephant, an ant moving a rubber tree plant.

The talks began in April after U.S. District Court Judge Susan Oki Mollway in Hawaii sided against the Navy and its claim that it couldn’t avoid sensitive whale habitat while conducting exercises that would drop a quarter-million explosives in the Pacific and blast sonar for half a million hours during five years of war games that started in January.

As a result of the negotiation with two plaintiffs, Earthjustice and the Natural Resources Defense Council, the Navy will now respect buffer zones around whale and dolphin habitat off both coasts at times when the animals congregate to forage, mate and raise calves.

Mollway’s decision was also a loss for the federal agency that granted the Navy a permit to operate with near impunity in a large area of the Pacific, even though the agency is charged with protecting marine mammals there as part of a congressional act to preserve them. The conservationists argued that the agency, the National Marine Fisheries Service, a division of the National Oceanic and Atmospheric Administration, failed to investigate possible alternatives that could result in less harm to animals.

In her decision, Mollway called the Navy’s dismissal of pleas to avoid whale and dolphin habitat because it was inconvenient to their plans “impractical.” The Navy’s “repeated reliance on sweeping, absolute statements that allow for no possibility of any restriction at all” is deficient, the judge wrote.

Mollway said the the court can’t substitute the judgement by the fisheries service with its own, nor could it limit the Navy’s area of operation or select marine mammal species it should avoid. “But … the Navy’s categorical and sweeping statements, which allow for no compromise at all as to space, time, species, or condition, do not constitute the hard look” that federal law requires in assessments of activity that could of possibly harm the environment.

The decision clearly suggested that the fisheries service dropped the ball in deferring to the Navy, said Michael Jasny, a policy analyst for the Natural Resources Defense Council. In Jasny’s opinion, the service isn’t entirely to blame. He said scientists there who work with activists were sympathetic to their arguments, but were overruled by executives in the Obama administration.

“It’s fundamentally a problem with government,” Jasny said. On one hand, an agency has a mission that isn’t a major priority for top officials. And “on the other hand, you have the Navy, one of the most powerful instruments in government.

“You had a canary trying to regulate an elephant,” Jasny said. In 2006, he recalled, “the canary pushed back” against a plan by the Navy to conduct exercises that would harm marine mammals. The service “got rolled over and hasn’t tried again. It’s focused on trying to get funds for research and not protecting marine mammals,” he said.

In a statement sent by a spokeswoman, Connie Barclay, NOAA said the “determination that the Navy’s activities would have a negligible impact on marine mammals was based upon the best available scientific information, and the fact that the authorized level of impacts [by the Navy] represented a conservative worst-case scenario.”

A spokesman for the Navy, Lt. Cmdr. William Knight, responded via an e-mail that said the fleet wants to be a “good environmental steward” while preparing for missions for national security. But it “is essential that sailors have realistic training at sea … that prepares them to prevail … with equipment that has been thoroughly tested. This training and testing contributes directly to the readiness of the fleet.”

Knight said the settlement with the activists preserved that. “The Navy has conducted similar training and testing activities in Hawaii and Southern California for over 60 years without evidence of major impacts to marine mammals,” he wrote. “The only marine mammal deaths in Southern California or Hawaii linked to naval training and testing occurred in March 2011 when a pod of dolphins swam into an explosives training event off San Diego, too late to halt the explosion.”

But in its environmental impact statement for the permit, the Navy claimed that explosives and sonar blasts would kill about 155 marine mammals and permanently injure about 2,000. Nearly 10 million would temporarily lose hearing in a way that disrupts their behavior.

A single “ping” from sonar every 10 seconds can forever damage the ears of animals that rely on hearing to find food in the deep black ocean, according to conservation groups that filed a lawsuit challenging the operation. There is no threat unless animals are within 100 meters of a ping.

“The ocean is a world of sound,” Jasny said. “Hearing is as important to whales and other marine life as seeing is to us. This repeated disruption on a broad scale of vital behavior … the science has made clear that it’s having serious effects.”

The disruption has shrunk mammal populations in points across the ocean, making them a place where “whales can scrape by, but find it hard to bring calves into the world and nourish them.”

David Henkin, an attorney for Earth Justice, said the settlement is a possible game changer that will pave the way for improved communications between the Navy and environmentalists. “This agreement establishes that the Navy can modify its training and testing to increase marine mammal protection, dispensing with the rhetoric the Navy has employed in the past that it cannot be done,” Henkin said.

He said the decision might also embolden the fisheries service and future presidential administrations to push back against the Navy’s request to kill and maim animals for war games.