The body of the southern resident orca — an endangered species in the United States — was discovered on Long Beach in Washington state in February, just days after HMCS Ottawa conducted sonar training exercises in the waters off Victoria, B.C.
A preliminary examination indicated significant trauma around the head, chest and right side of the orca known as L112, but results of necropsy and pathology tests and a scan of the animal's head are incomplete.
Just hours after the navy sonar tests were heard, southern resident killer whales were spotted in the same area in the Haro Strait that divides Canada and the United States.
The law enforcement office of the U.S. National Oceanic and Atmospheric Administration, or NOAA, has launched an investigation into the death.
Brian Gorman, with NOAA's National Marine Fisheries Service, said investigators haven't made a connection between the naval exercise and the death of the whale.
"That's the first thing we have to determine. Depending on where this investigation leads, I suspect (the investigation) may extend to the Canadians or it may not."
Gorman said the investigation will attempt to determine if there's been a violation of the U.S. Marine Mammal Protection Act.
Scott Veirs, an oceanographer and the president of Beam Reach Marine Science and Sustainability School, has been trying to piece together the puzzle of L112's death and hasn't ruled the Canadian navy out.
"To me it's the most plausible connection," he said in an interview. "It's a difficult but wonderful detective story to try to interpret for the public."
But he also admits that researchers may never know how the animal died.
Veirs and his students have been going over acoustic recordings during the early February exercise to determine where the killer whales were when the sonar went off.
They also heard several large explosions at the same time as the sonar, but haven't been able to confirm if explosives were used in the navy's war games.
No one at the Department of National Defence or Defence Minister Peter MacKay's office returned a request for an interview.
While he's pleased that NOAA has launched an investigation into the death of L112, Veirs wonders why there isn't a similar investigation in Canada.
After the whale's death, Veirs joined more than two dozen environmental groups and 20 whale biologists and other experts on both sides of the border to write to the Canadian and American governments asking for a total ban on naval training using sonar in critical killer whale habitat off the West Coast.
The letter sent to the U.S. Secretary of the Navy Ray Mabus said the American and Canadian navies must work together to protect the species.
"It is simply unacceptable for Canadian naval operations to compromise the Endangered Species Act and Marine Mammal Protection Act and by the U.S. Navy's own procedures."
Just 87 of the rare southern resident killer whales remain in the U.S. No one is allowed to approach one of them within 200 yards or 183 metres, and they must stay out of the path of whales by 400 yards, or 366 metres.
In Canada, the whales are listed as a species at risk, making it illegal to kill or harass the animal. Canada has regulations keeping boats a certain distance from the whales, but is only now considering laws that would enforce a 100-metre exclusion zone around the whales.
The letter sent to Canada's defence minister said the whales were seen within the same area as the Ottawa just hours later.
"This incident underscores the need for stronger protection of these whales, especially within their critical habitat," the letter stated.
The navy's sonar mitigation is based on its ability to maintain a safety zone of 4,000 yards or about 3.6 kilometres.
"Yet southern residents are known to fall completely silent when resting — sometimes for periods of six hours or more — and can be difficult to sight even during the day beyond a few kilometres," the letter noted.
The letter said the Navy's current measures fail to take into account the wide-ranging impacts of the mid-frequency active sonar on the whales and called for the establishment of acoustic sanctuaries in the killer whales' critical habitat areas.
Thirty six hours after the sonar was set off, a group of southern residents from unusually mixed pods was seen in the sheltered waters of Discovery Bay, west of Port Townsend, Wash., an area they had never been seen in decades of whale watching by experts.
That strange behaviour is one of the reasons Robin Baird, a research biologist with the Cascadia Research Collective, signed on to the letter asking to silence sonar.
"That's an area where southern residents have never been recorded in," he said. "It's the kind of place if the whales were the area would duck into in order to get away from the sound."
Baird said his biggest concern is the use of explosives in such war games.
"I think just as a concerned citizen that we should not be dropping bombs or blowing things up where we've got animals of any kind, let alone this apex species that's loved by millions and millions of people."
Joe Olson, the president of Cetacean Research Technology, was another of the 20 biologists and wildlife experts who signed the letter.
Olson said loud noises such as sonar frighten and confuse the whales.
He said when the U.S. Navy's USS Shoup set off its sonar in July 2003, several witnesses watched the whales scatter or come to the surface.
"The whales were acting totally bizarre. They were hiding from the sound on the surface, because when you get to the surface the sound starts to reflect back downward."