As a seafood restaurateur and founder of Sawyer Culinary Adventures, Louie Sawyer sought out exotic tastes for his intrepid Western clientele. During a scouting trip to Hong Kong in 2013, he and five associates dropped by a major shark fin processing facility, run by a short, fast-talking kingpin who goes by the name of Mr. Eddie.

All 14 of the species most prevalent in the shark fin trade are classified as threatened or nearly threatened, partly due to Chinese consumption of shark fin soup, but Hong Kong’s teeming markets are insensitive to this fact. Cluttered storefronts also openly sell endangered sea horses and hawksbill sea turtles, along with elaborate elephant tusk carvings. Mr. Eddie’s operation—“the Walmart of the endangered-species trade,” Sawyer called it—is not in the habit of welcoming camera-toting foreigners, and Mr. Eddie was initially suspicious of the group. He scrutinized their business cards and peppered them with questions. As his gruff manner grew more intimidating, one of Sawyer’s colleagues suggested they ought to leave. It wasn’t until they made for the door that Mr. Eddie relented. “No, it’s OK. Come, come. I show you around here.”

SHAWN HEINRICHS / BLUE SPHERE MEDIA

Sawyer’s crew had reason to feel uneasy, considering that their identities were, in fact, a ruse. Louie Sawyer was actually Louis Psihoyos, an activist filmmaker whose first documentary, The Cove, exposed the clandestine slaughter of dolphins in a Japanese seaside town, earning an Academy Award in 2010. His second film, Racing Extinction, airing on the Discovery Channel on December 2, takes up the man-made causes behind what biologists call the sixth mass extinction—the spate of plant and animal losses that threatens to eradicate up to half of all living species on Earth within this century.

During the same week they were in town to collect their Oscar for The Cove, Psihoyos’ team conducted an undercover sting of a Santa Monica, California, restaurant that served whale meat, ultimately shaming the restaurant into closing. Among other stunts portrayed in Racing Extinction: They posed as importers of fish oil supplements to infiltrate a mainland Chinese shark dealer; captured unprecedented footage of humans swimming alongside migratory blue whales in Mexico; and, using a Tesla retrofitted with a powerful projector, blasted the sides of US corporate facilities with images of the animals that their business activities are said to endanger.

SHAWN HEINRICHS/BLUE SPHERE MEDIA

In Hong Kong, Mr. Eddie led Psihoyos and his undercover team across an alley to a building with a shark sculpture hanging off the facade. He typed a code into a keypad and slid open the front door to reveal a storage room filled with bags of dried sea creatures. On the walls hung posters that identified various shark species and the characteristics of their fins, which fetch up to $2,000 a pound on the Asian market. Psihoyos and three accomplices wore tiny pinhole cameras disguised as shirt buttons, which had been provided by a specialist who designs covert video surveillance gear for human rights groups and law enforcement agencies. In China, merely wearing such devices is grounds for imprisonment. Two others with Psihoyos, including Shawn Heinrichs, a cinematographer and marine conservationist who’d been kicked out of Mr. Eddie’s facility before for attempting to film, wore digital SLR cameras dangling around their necks, discreetly capturing video.

“It is hard to catch a shark, you know?” Mr. Eddie told the group. “If you get the shark, every part of the shark can be sold for money. So we are not going to throw away any meat from the shark. But a lot of the greenie people, they are misunderstanding our industry. They think we take the fin and let the live shark go down into the sea and die struggling like this. You know, very bad. But that is not the truth. That video is made by the greenies themselves.”

Mr. Eddie was referring to videos like the widely circulated PSA about shark fin soup, created by the environmental organization WildAid and starring Chinese basketball star Yao Ming. It showed a tawny nurse shark in Indonesia lying on the seafloor with its fins dismembered, desperately trying to swim. Heinrichs, who was standing next to Mr. Eddie, had actually shot that footage. Psihoyos and the others made a show of agreeing with Mr. Eddie’s opinion of environmentalists, and the ice was broken. They were in.

Next, Mr. Eddie brought them up to a roof. Against a scenic maritime backdrop stood rack upon rack of severed shark fins—thousands of them—laid out to dry under the sun but out of public view. “Somebody can tell you that there are 70 million sharks being killed for the fin trade every year, but when you actually see the evidence and witness this gorgeous animal being reduced to piles of appendages, there’s a horror that becomes rage,” Psihoyos says later. “Especially when you know it’s a nutritionless and tasteless fabrication from a bygone era.” Downstairs, in a small showroom off the street, wood-paneled cases displayed dried sea animals. Mr. Eddie held up a worm. “44,800 US dollars per kilo,” he boasted. “44,800. It is a wholesale price! They believe—that’s why I say, they believe—it can cure cancer.”

He grinned. “Chinese have a lot of beliefs.”

This eco-vigilante approach has become Psihoyos’ signature brand of filmmaking. “The Cove was the result of watching too many James Bond movies and Jacques Cousteau specials as a kid,” he says. The film wrapped an environmental documentary around a caper flick—PBS meets Ocean’s 11. A reviewer for The New York Times called it “one of the most audacious and perilous operations in the history of the conservation movement.”

Psihoyos wears such descriptions as a badge of honor. “Most documentaries feel like you’re going to a medical lecture, where you’re just getting a lot of facts but there’s no story. The goal is to be a fly on the wall,” he tells me at a Santa Monica hotel, after a late night spent at the Port of Los Angeles projecting blue whale images from the Tesla. (Between 1988 and 2012, there were 100 reported cases of large whales struck by ships along the California coast.) “But if you can wrap that around a tale of adventure, of thrill and redemption, and tell a really goddamned good story, people will listen to almost anything. When people see our films, I want them to feel like they landed in a different world, like, this is not my beautiful life. We’re trying to wake people up to what is actually going on.”

Psihoyos is 58, with silver hair and an unassuming Midwestern accent. He describes Racing Extinction as “a real-life Avengers.” In the film, he visits the scientists and activists working on the front lines of a global catastrophe: Earth, they tell us, is losing species 1,000 times faster than the natural rate of extinction. The baiji river dolphin, Western black rhino, and golden toad are among the disappeared in recent years; the population of Maui’s dolphins in New Zealand has plummeted by half since 2004—there may be as few as 43 of them left. Blue whales in the southern oceans are down to just a fraction of historical levels, and plankton production is just 40 percent of what it was a half century ago. Forty-one percent of all amphibians are considered threatened. “We’re losing species faster than we can describe them,” Psihoyos laments. “When you’re talking about losing all of nature, it’s no longer a spectator sport. Everybody has to become active somehow.”

Psihoyos came to his own activism by way of journalism. In the mid-1970s he was among a breed of so-called concerned photographers—“a highfalutin name for people who try to affect social issues with photography,” as he puts it. His early subjects included Pete Seeger, who was then campaigning to clean up chemical pollutants in the Hudson River. Psihoyos recalls sitting around a campfire with the folksinger and other musicians after a concert. “These people were trying to dream of a better world,” he says. “And they actually made it happen.”

In 1980, Psihoyos was hired by National Geographic. His first assignments for the magazine were to document the rise of recycling and the environmental fallout of Wyoming’s energy boom. He shot four stories around the world about the Mesozoic era—the age of dinosaurs—assignments where “extinction was always in the back of your mind.” He soon earned a reputation for elaborately constructed portraits and expensive conceptual projects. For a 1995 feature on the information revolution, Psihoyos had Bill Gates hoisted 55 feet above a forest floor in a sling, over a tall stack of paper, to demonstrate the volume of information that at the time could be stored on a single CD-ROM.

“To be able to see this hidden world, it’s like you’re let in on a magic trick, but the magic trick is actually killing the planet.”

Psihoyos befriended Jim Clark, founder of Silicon Graphics and Netscape, while shooting his cover portrait for Fortune. At the time, Clark was building a 155-foot sailing yacht named Hyperion. The two became scuba buddies. Clark took Psihoyos to some of his favorite dive spots around the world. In Papua New Guinea, they encountered a once-thriving reef in a state of ruin. During a trip to the Galápagos Islands, they watched as longline fishermen pillaged a protected marine sanctuary. “Jim turned to me and said, ‘Somebody should do something about this,’” Psihoyos recalls. “And I said, ‘We’ll use your money and my eye, and we’ll make films.’”

In 2005, Clark provided the seed money to fund the nonprofit Oceanic Preservation Society, installing Psihoyos as its executive director. Clark then built what Psihoyos calls the best underwater camera in the world, which has an 80-megapixel sensor and a custom-fitted glass dome that produces no color aberrations. “We call it the doomsday camera, because we take this camera and document the best surviving reefs in the world, in a resolution that nobody’s ever been able to see,” Psihoyos says. “My entire career is built on this notion that we can show people something they haven’t seen before in a way that they’ve never visualized—images that make it impossible for people to forget.”

https://www.youtube.com/embed/-AHbNMXhCF8

The story of mass extinction is in part a story about global warming, whose main cause is ubiquitous yet mostly invisible to the human eye. So in Racing Extinction, Psihoyos employs an infrared camera fitted with a color filter that brings into stark relief the sources of carbon dioxide in our environment—the lawn blowers, smokestacks, and parades of smoldering tailpipes on a rush-hour freeway. Seen through the camera, an Airbus 380 gliding down the runway at LAX appears dragonlike, billowing gas. In a voice-over, Psihoyos reflects: “To be able to see this hidden world, it’s like you’re let in on a magic trick, but the magic trick is actually killing the planet.”

The black Tesla Model S is parked a bit too conspicuously across from the Shell oil refinery in Martinez, California, a sprawling complex of scaffold towers and gaseous plumes that resembles a launchpad. It’s late one night in March 2014, and the road is quiet. Two GoPro cameras are aimed at Leilani Münter, a dark-haired Nascar driver who races under the moniker Carbon Free Girl and who sits behind the wheel of the Tesla in black faux-leather pants and pumps. The rear seats have been stripped and replaced with a 24-volt lithium-ion battery pack and solid-state drive. The back window has been removed to install a 15,000-lumen video projector mounted on a retractable steel frame that can extend and pivot in any direction like the artillery cannon on a Batmobile.

ANDREW ECKMANN

The Tesla retrofit is the brainchild of Travis Threlkel, a former techno-psychedelic-folk rocker who cofounded Obscura Digital, a San Francisco company that has pioneered immersive-projection and object-mapping technologies, real-time holographic displays, and Minority Report-esque multitouch displays. For scenes that appear in Racing Extinction, Threlkel’s team orchestrated rogue projections of endangered species across New York City. Sharks swam across the facade of the Stock Exchange; the words “Acidifying the Oceans” ran like a news ticker along the exterior of the David H. Koch Theater at Lincoln Center. During last year’s Climate Summit, with permission from the United Nations, Obscura projected a vivid short film about extinction featuring Jane Goodall onto the iconic Secretariat Building. Throngs watched from the sidewalks. “With projection you can make people see things in new ways,” says Threlkel, wearing cowboy boots and a vintage polyester shirt. “Once you break out of the rectilinear format, the observer is more open to getting a message.” The filmmakers bought the Tesla after meeting with Elon Musk himself, who appears in Racing, and Obscura embellished the exterior with a coat of electroluminescent paint, which can toggle the car’s color from black to luminous blue when a current is applied. “It’s like a modern-day Bond car,” Psihoyos says.

The crew has permission from the city of Martinez to film the Tesla “and trains,” although the part about trains was of course a feint. They are here to capture their own projections of the chemical symbols of hazardous air pollutants onto the refinery’s towers.

Within 10 minutes, a security guard appears across the road in the empty parking lot of a liquor store. Two Contra Costa County Sheriff cars arrive soon after, followed by two men in a truck with amber warning lights, who step out in red jumpsuits emblazoned with the Shell logo. Psihoyos and his coproducer, Gina Papabeis, talk to the authorities as the film crew slyly rolls the camera from a distance. Handing over the permit, they explain that they are there to film an electric car promotion.

Papabeis wears a button camera, while Psihoyos holds a plastic water bottle that conceals a tiny videocam. The Shell guard explains that the US Department of Homeland Security now regards oil refineries as critical infrastructure, and anyone caught filming them must be reported.

Psihoyos denies any such intention, but gesturing to the towers looming beyond the fence across the road, asks, “What if we photographed your smoke?” The Shell guard quickly corrects him, saying that the heaving emissions are only steam. Looking down at the phone in his hand, Psihoyos begins reading off the names of chemicals that oil refineries are known to release: “Sulfur oxide, nitrogen oxide—”

His coproducer wears a button camera, while Psihoyos holds a plastic water bottle that conceals a tiny videocam.

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“For someone who’s not here to film a refinery, you sure seem to know a lot about them,” the guard says. (Psihoyos tells me later, “There might have been a minute of theater in there, but I just wanted to get him to think.”) It’s time to move on. The crew retracts the projector, and Psihoyos drives off with Münter in the Tesla.

A few days later, we’re sitting by the pool at a Santa Monica hotel as Psihoyos recounts a story that occurred 30 years prior but still seems to haunt him. While living as an artist in New York, he drove one weekend down to a flea market in Perkiomenville, a town outside Philadelphia, to collect found objects. A family of four walked ahead of him, past tables of antiques and junk. Psihoyos noticed a pickup truck with large side mirrors pull up behind them. “I could see from my angle that this mirror might hit the family,” Psihoyos recalls. “It’s a busy flea market, people are laughing, there’s music going. I started to scream, and I felt people looking around at me like, what are you doing?” And so Psihoyos muted himself. “Do you ever scream in public?” he asks. “No, it’s very uncomfortable.”

It was just a moment of self-conscious silence. But by the time Psihoyos gathered himself and yelled out again, the truck’s side mirror had smacked the son and daughter, knocking the children down beneath the vehicle. “They died right in front of me,” Psihoyos says. His lips are quivering. “Blue-fucking-sky day, and I realized that it was my weakness. This family was crushed; two lives were extinguished. And it was because I was too fucking embarrassed to scream in a crowd.”

Psihoyos brushes a tear with his finger, becoming more impassioned. “Now, if you believe that we’re losing half the species on the planet and it’s because of our behavior? If we’re burning oil because it’s cheap? We’re losing this world before we have a chance to understand that it’s here. I think about that family that died because I couldn’t speak up, and now I look at my whole world dying. Everything that we’ve known. I don’t mind being the guy screaming in the room at this point. If I can tell it in a beautiful, elegant way and take people on an interesting ride, I’ll scream as loud as I can.”

Andy Isaacson (@andyisaacson) is a writer and photographer living in New York.