On the day before Thanksgiving, 2011, Greg Rouse, a trim marine biologist in his fifties, was tidying his lab at the Scripps Institution of Oceanography, in La Jolla, California. Rouse studies the worms and other small animals that inhabit the deep sea. He was organizing his microscopes, dissection supplies, and jars of deep-sea critters when he received a long-anticipated e-mail.

In the late two-thousands, Rouse and Eddie Kisfaludy, then an operations manager for Virgin Oceanic, had begun meeting with officials from the National Oceanic and Atmospheric Administration (NOAA) and the city of San Diego to pitch an alternative approach to the disposal of dead whales. Often, whales that wash up on shore are hauled to landfills or pushed back into the water. Rouse and Kisfaludy wanted to tow one out to sea, sink it to the seafloor, and watch what happened. Whale falls, as marine biologists call such events, create pop-up habitats that may serve as stepping stones for organisms migrating from methane seeps or hydrothermal vents to other parts of the ocean. Precisely how this works, and which species colonize the carcass as it degrades, were open questions that Rouse hoped to answer.

In the e-mail, a biologist from NOAA wrote that a large female fin whale had washed ashore four days previously, on the rocky beach at Point Loma, just west of downtown San Diego. The NOAA team had already moved the carcass to the protected beaches of Mission Bay and performed a necropsy, concluding that the whale had been hit by a ship. Now they were ready to hand it over to Rouse: if he could mobilize the necessary resources on short notice, the whale was his to sink.

Rouse quickly met up with Kisfaludy to strategize. They needed a boat big enough to tow a sixty-foot, twenty-three-ton whale, so Kisfaludy leaned on a Newport-based friend, Chris Welsh, for the use of his large catamaran. To sink the carcass, they sourced five tons of rusty chains from Newport Harbor and another two tons of iron shackles from the Scripps scrap yard, in San Diego.

On Thanksgiving morning, Welsh set out in his catamaran—rusty chains on board—and sailed south. The next day, he met up with Rouse, Kisfaludy, and a growing group of intrigued friends at the dead whale. It rested on the sand, immovable. At high tide, however, the carcass began to float, and the team made its move. They tied seven ropes around the whale’s tail and sailed west. Several hours passed. The weather was crisp and sunny, and there was little boat traffic. To Rouse’s surprise, the whale had attracted no scavengers, despite its exposed rolls of dark purple muscle draped in white, translucent fat. The team began to consider names for the whale. Someone suggested Rosebud, and it stuck.

At the drop zone, the team tied the ropes to the hunks of metal, then used the boat’s crane, normally used to launch submarines, to lower the weight into the water. After a few hours and a lot of splashing, all of it was deployed—but Rosebud bobbed on the surface, refusing to sink. Rouse noticed a large gas bubble gathering inside the whale’s throat. “We were struggling with what to do,” he recalled, by phone. They wondered if they could release the trapped gas by stabbing holes in the carcass, but, Rouse said, “all we had was a kitchen knife attached to a stick.” Kisfaludy and Welsh, dispatched on a dinghy, tried to free the gas, with no success. Then the afternoon breeze picked up. As the swell grew, the whale rocked back and forth. Eventually, the bubble popped out of its mouth, along with a pile of guts. The team cheered, delighted and disgusted. Rosebud disappeared beneath the waves.

Rosebud had sunk just twelve nautical miles from San Diego, but, in deep-sea research, close and accessible are very different things. The whale had fallen to a depth of eight hundred and fifty metres—about half a mile. Most of the remotely operated vehicles, or R.O.V.s, capable of conducting intricate operations at that depth are owned by oil companies; only a handful are available for scientific research. Such research expeditions can cost as much as fifty thousand dollars a day, and securing that much funding and ship time can take years. Rouse’s approach had been to sink Rosebud first and hope that scientists would find a way to visit it in the future.

In 2012, Paul Allen’s superyacht, Octopus, conducted some initial reconnaissance. In 2013, Rouse participated in an expedition mounted by the Monterey Bay Aquarium Research Institute (MBARI) to study animal and microbe dispersal patterns at Rosebud and other nearby habitats.

In the middle of 2014, Rouse joined another MBARI expedition. (In total, there have been five expeditions to Rosebud.) At the time, I was a graduate student at the California Institute of Technology, studying the microbial activity around methane seeps. Whale falls and methane seeps can support similar flavors of microbes; I jumped at the chance to come along.

On a breezy June morning, we set out aboard the Western Flyer, a boxy white ship run with the no-frills efficiency of a floating industrial platform. As we lurched out of San Diego, I frantically set up a shipboard lab, preparing chemicals and sampling jars. By the time we reached Rosebud’s location, the wind had risen and the seas had grown choppy. Belowdecks, the cresting waves reverberated between the twin hulls. Using a compact crane, engineers lowered the jeep-sized R.O.V. into the moon pool, an opening in the deck that offers entry into the water.

I pinballed through the narrow corridor to the control center to watch the descent. As my eyes adjusted to the dark room, I saw that it was illuminated by a wall of about a dozen screens: one showed a tense World Cup match between Italy and Costa Rica, while the rest contained camera views from the R.O.V.—shades of blue fading to the black of the deep sea. Eventually, the R.O.V.’s lights illuminated a uniform brown plain punctuated by occasional red rockfish. The camera began to move across the seafloor toward Rosebud.

We knew, broadly, what had happened in the preceding three years. For denizens of the seafloor, a whale fall is like a Las Vegas buffet—an improbable bounty in the middle of the desert. Rosebud had delivered about a thousand years’ worth of food in one fell swoop. The first animals to pounce had been scavengers, such as sleeper sharks and slimy, snake-like hagfish. In the course of about six months, they had eaten most of the skin and muscle. Inevitably, the scavengers had scattered pieces of flesh around the whale carcass, and native microbes had multiplied quickly around those scraps. Their feeding frenzy, in turn, had depleted oxygen in the seafloor’s top layers, creating niches for microbes that could make methane or breathe sulfate.

As Rosebud came into view, we saw colorful microbial carpets light up the screens—plush white, yellow, and orange mats, each a community of microbes precisely tuned to their chemical milieu. The whale’s towering rib cage had become a cathedral for worms, snails, and crabs, which grazed beneath its buttresses. A few hungry hagfish slithered through the skull’s eye sockets. When the cameras zoomed in, we saw that the bones were covered in red splotches. Rouse leapt from his chair and rushed to the monitors for a closer look: he suspected that the red tufts were colonies of remarkable bone-eating worms called Osedax, which had only just recently been described in a rigorous scientific study.