If such a useful molecule was abundant underground, the researchers reasoned, then the deep biosphere might be even more diverse and widespread than expected. And whatever was generating dark oxygen might also be found on planets or moons beyond Earth. “We started digging,” Ruff told me. His team soon discovered trace amounts of oxygen in deep groundwater from around the world. They found DNA from aerobes—microbes capable of using oxygen—in places that sunlight could never reach. Other microbes seemed to produce their own dark oxygen, perhaps to extract energy from hydrocarbons such as methane, much as drag racers inject nitrous oxide into their engines to boost horsepower. Last year, Ruff and five other investigators won a multimillion-dollar grant from NASA to extend their investigations on a sort of dark-oxygen world tour. Moab Khotsong was their first and deepest stop.

Once the Cage was moving at full speed, it raced down the shaft at nearly forty miles an hour. It was a remarkably smooth ride, apart from a faint rattle and whoosh each time we passed an underground level. Our ears popped; the researchers chuckled nervously. Cool water began to drip from the ceiling. Finally, about four thousand feet below the surface, the lift slowed at our first stop.

Before we could visit the super-salty radioactive brine at the bottom of the mine, we had to collect a baseline sample of groundwater that was not a billion-plus years old. We exited the Cage, ducking through a curtain of falling water, into a high tunnel. No natural rock was visible here; the passageway had been plastered over with mottled concrete and lined with air pipes. It smelled of rotten eggs and concrete dust. At first glance, it seemed utterly devoid of life.

Bennie Liebenberg, a former geologist at the mine who was serving as our guide, has the plodding, slightly wide-eyed manner of someone who has spent a lot of time underground. He previously facilitated the drilling of the borehole after the earthquake, and has been the mine’s liaison with scientists ever since, helping convince higher-ups that the chance to solve profound environmental mysteries was worth the occasional disruption to mining operations. In his office, he keeps a copy of “Deep Life” that Onstott inscribed: “You have been a blessing to our cause. Eternally grateful.”

Liebenberg led us to a wall where water was gushing out of orange pipes. It had been flowing this way since the shaft was drilled, decades earlier. “They tried to seal it, but couldn’t,” he said, in a clipped Afrikaans accent. The water here was shallow enough to have been connected with surface flows tens of thousands of years ago, and it still contained oxygen. Thus, it would give the scientists a point of comparison with the billion-year-old brine below. Before the researchers could start sampling it, though, a deafening roar suddenly filled the tunnel. Scott Wankel, the team’s lead geochemist and a researcher at the Woods Hole Oceanographic Institution (W.H.O.I.), had accidentally kicked a tiny hole in a rusty pipe of compressed air. (“You broke the fucking mine, dude!” Ruff joked later; Liebenberg seemed unconcerned.)

We had earplugs, thankfully, but we were no longer able to speak. Instead, for several hours, the scientists mimed awkwardly as they collected samples: No, I don’t need that small bottle, I need the slightly smaller one! Eventually, someone realized that we could write notes to one another, which helped move things along. Lloyd, the U.S.C. geobiologist, gestured for me to give her my notebook.

“Did you see the sulfur streamers?” she wrote. I shook my head. She waved me over to a gutter where tufts of blue-gray fibres were fluttering in mine water. “They are giant filaments of sulfide oxidizing bacteria,” she wrote on pages that were getting increasingly wet. Apparently, some bacteria were using oxygen in the tunnel to metabolize sulfur compounds in the water, and that was producing the rotten-egg smell. Single-celled organisms ganged up in filaments, by the tens of millions, to avoid being carried away by the flow.