How does an 18-foot-long, 2,000-pound carcass just disappear?

That question has puzzled some divers and photographers who regularly plunge into the waters off San Diego.

It started earlier this spring when Doug Bonhaus took advantage of some calm weather to scuba dive in Scripps Canyon. As he descended, a hulking mass took shape below him.

There, at an exceptionally shallow 115 feet, lay the body of a baby gray whale.

Whale falls are usually not seen by human divers. Typically, they are discovered by remotely operated vehicles at depths exceeding 3,000 feet.

Local marine biologists had a guess as to the gray whale calf’s origins. An animal that matched what was found on the seafloor had been spotted swimming near La Jolla Shores, desperately searching for its mother. During its final hours, it was seen approaching boats, as though asking for help that wasn’t coming.

Because it was the first time in memory that a fall was so accessible to people, other divers quickly made their way to the site. Among them was Jules Jacobs, an underwater photojournalist who has written for The New York Times about his explorations.

At that point in late January, the carcass’s resting place was a trough in the canyon that required pinpoint precision to reach. So Mr. Jacobs steeled himself for a dangerous and mentally taxing dive.

Navigating the crepuscular gloom with a team of five other divers, the dive lights suddenly illuminated what he was looking for: the mottled-skinned, emaciated calf. The calf’s eyes had already succumbed to the elements; it seemed locked into an expression of sorrow.

“It’s humbling to dive a whale fall where the tail alone is as big as your body,” Mr. Jacobs said.

Mr. Jacobs planned additional dives to observe the animal. On his second visit a week later, a chunk of the animal’s tail was missing, likely the work of scavenger sharks like the seven gill or the mako.

After a surge of spring storms, Mr. Jacobs descended into freezing blackness for the third time in late February. Gripping his camera gear so tightly his knuckles turned white, he waited for the decaying animal to appear.

What he found was only the barren seabed.

The calf was gone.

Gray whales, which can grow to around 45 feet in adulthood, have a migration that is the one of the longest of any mammal. It starts in the balmy seas of Baja California and extends to feeding grounds in the high latitudes of the Arctic Oceans. The calf and its missing mother were most likely headed north before they were separated. During this phase of the journey, they would have been at their most vulnerable, with the mother not having eaten for six months.

Gray whale populations follow a boom-and-bust cycle, with numbers crashing and then recovering, and sometimes up to a quarter of the population lost in a few years.

For about six years, however, the population has failed to rebound as it did during previous die-offs. Scientists attribute this decline to climate change, which accelerates Arctic warming and disrupts the gray whale’s prey. Ship strikes and entanglements in fishing lines aggravate losses to starvation.

“We’re unlikely to return to a world that can support 25,000 gray whales anytime soon,” said Joshua Stewart, an assistant professor at the Oregon State University Marine Mammal Institute. Dr. Stewart expects to see many more whales dying on the West Coast.

Still, in the normal course of events, the death of a whale does not always signify an end. Instead, it catalyzes new beginnings.

A riot of life blooms from a whale carcass, even a calf’s. The flesh nourishes scavengers, the bones are colonized by microbes and worms and the curved vertebrae form new highways for a rapidly developing reef.

“A whale fall is a real bonanza and may provide as much food as normally reaches the sediment beneath it in 200 years,” said Craig Smith, professor emeritus of oceanography at the University of Hawaii. “Ironically, we know more about whale-fall communities in the deep sea than in shallow water.”

A whale decays in three ecologically distinct stages. First come the scavengers — sharks, crabs, hagfish — which tear into the soft tissue. Then, along come the worms in “huge, writhing masses in the organic-rich ooze surrounding the carcass,” Dr. Smith said. This can last seven years in what scientists call the enrichment-opportunist stage.

Finally, bacteria deep within the bones produce hydrogen sulfide, fueling the chemosynthetic bacteria on the surface of the bones and those living symbiotically inside animal hosts. This stage can last decades, with more than 200 marine species thriving on a single whale fall.

But this infant whale and its carcass had vanished. Had something or someone made off with it, preventing that life-sustaining whale fall from continuing?

Gregory Rouse, a marine biology professor at the Scripps Institution of Oceanography, believes the explanation is less mysterious. During whale falls, he said, decomposition in the body cavity generates gas, which can cause the carcass to rise again after initially sinking, and float before eventually settling on the bottom.

Strong winds and pulsing currents likely swept the body deeper into the canyon, which descends as far as 1,600 feet down.

“This animal would’ve grown into a titan, but its life was snuffed out in infancy,” Mr. Jacobs said.

But where it lies quietly in the darkness, new life may proliferate and prosper.