A silver van rolls slowly down a narrow road on the edge of Bayfield. With its darkly tinted windows and government plates, the van has an ominous appearance, and impatient drivers pull around the creeping vehicle. Just behind the high school, the van stops.

A door swings open, and Gabrielle Petron, a scientist with The National Oceanic and Atmospheric Administration and the Cooperative Institute for Research in Environmental Sciences at the University of Colorado, hops out, gesturing to journalists to pull over. Speaking with a French accent, she explains that the van’s sensors indicate the presence of above-background levels of methane, a potent greenhouse gas.

It’s not hard to find the probable source. Inside a chain-link-fenced enclosure next to the school’s tennis court, a BP America natural gas well juts from the ground. Everything’s painted gold and purple, the school colors, with “Wolverine Pride” emblazoned on a metal box. Like many of the 40,000 oil and gas wells in the San Juan Basin, this one extracts natural gas from the Fruitland coal formation. The gas, which is largely methane, is gathered here, processed and piped to market. Or at least most of it is: Some of that methane is leaking from the wellhead and drifting into the atmosphere, contributing to the Four Corners Methane Hot Spot, a plume of greenhouse gas that hovers over the region. When scientists noticed the hot spot a decade ago, they thought their equipment was malfunctioning. But more imagery from 2009 confirmed its existence, and in 2014 it garnered national attention.

The suspect behind the hot spot is the oil and gas infrastructure. Other known contributors include an underground coal mine, from which methane is vented, and a few landfills and two coal-burning power plants.

But there’s a 155,000-ton gap between the emissions these facilities report to the EPA’s greenhouse gas inventory, and the amount of emissions the scientists estimate is needed to produce the hot spot. Petron and scientists under NASA and NOAA, descended on the region this spring, using planes, satellites and automobiles to account for all that methane.

What they find could have wide-ranging implications. Natural gas emits about half the carbon per unit of energy generated as coal, and about a third less than oil, making it a good “bridge” from a coal-heavy system to one that’s carbon-free. Yet the main ingredient of natural gas –methane – has 30 times more global-warming potential than carbon dioxide. If scientists find that natural gas is behind the extra emissions, it could cloud the fuel’s climate-friendly status. It might also indicate how hard the region’s oil and gas industry will be hit by regulations to reduce emissions by 45 percent.

The industry blames the gap on geologic seeps, where methane leaks unbidden from the earth, as it has done for millennia. Environmentalists scoff at the theory, but researchers aren’t discounting it. “The seeps are definitely a piece of the puzzle,” says Devin Hencmann, with LT Environmental, which monitored the seeps in the San Juan Basin for the past decade.

But just how big a piece? And where does it fit into the hot spot puzzle?

A few hours before her stop in Bayfield in April, Petron and her assistant, Eryka Thorley, show a couple of journalists around the van. It sits in the parking lot for the popular Carbon Junction trailhead. The Animas River – not yet polluted by the mining spill in August – runs by below, and just beyond it looms Carbon “Moving” Mountain, so nicknamed because, in the 1930s, it grew violent for several months, shifting and sliding.

A computer monitor mounted on the van’s dash reveals concentrations of carbon dioxide, methane and carbon monoxide in the air. In the back are more instruments for capturing air samples.

In pre-industrial times, the background level of methane on Earth was about 750 parts per billion. In about 1850, that level shot up, and now it’s about 1,800 parts per billion, or 1.8 parts per million. In the parking lot, the methane line jumps up and down with shifts in the wind, but remains higher than background levels, rising to 5 or more parts per million.

The nearest natural gas or oil well is at least a mile away. There are no coal mines nearby, no feedlots, landfills or any other common source of methane. But then again, there doesn’t need to be. The parking lot sits in a notch, formed by the Animas River, in the Hogback Monocline. Petron leads points to an outcrop of the Fruitland coal formation, the souvenir of a swamp that lurked along the shores of a receding sea 65 million years ago. It’s brimming with methane, some of which is leaking out here. This methane was infeasible to extract until the 1980s, when government-subsidized technology and tax credits made it a moneymaker. That launched a boom that would make the San Juan Basin the nation’s top coalbed methane producer.

In 1993, a resident of the Pine River Ranch subdivision north of Bayfield complained to Colorado regulators that, after 10 years of providing clean water, his well had begun spewing methane. Similar phenomena had been reported in other parts of the basin, but this one was different. Investigators couldn’t find leaky or badly cased gas wells nearby, but they noticed that the house and well were located along a low point in the Hogback Monocline, where the Pine River had eroded through it, right on top of the Fruitland outcrop. The methane, it appeared, was coming straight out of the coalbed.

Such natural seeps had been witnessed along the outcrop for a century, but they were getting more intense. Trees and bushes began dying off in Carbon Junction. Near Valencia Canyon Gap on the Southern Ute Indian Reservation, methane emanated with enough pressure to fling grains of sand several inches into the air, and hydrogen sulfide levels, at a hazardous 200 parts per million, forced the closure of a nearby road.

Things got worse. Within a year after the changes were observed, “a half-mile long by 50- to 75-foot wide swath of previously healthy piñon and juniper trees, sagebrush and saltbrush stood dead as stark testimony to recent environmental changes,” lamented a comprehensive 1999 Bureau of Land Management report on the issue. Methane was seeping from some spots at 100 percent concentration. Methane invaded more wells and pooled in the crawlspaces of homes.

The Colorado Oil and Gas Conservation Commission formed a team, and concluded in 1995 that the most likely explanation for the sudden increase in methane seep at the subdivision was the “dewatering” of the coal seam. Unlike “conventional” reservoirs of oil and gas found in sandstone or shales, coalbed methane is adsorbed, or bonded, to pores in the coal by water pressure. In order to “liberate” methane, drillers pump out the water from the coal seam. By 1999, just a decade after the boom had begun, coalbed methane wells on the Colorado side of the San Juan Basin alone had produced over 10 billion gallons of water, freeing the methane to escape from the outcrop.

Amoco – now BP, the biggest operator in the region – pushed back. They posited that drought or an increase in domestic wells was drying up the coalbed and liberating the methane, or an uptick in precipitation was causing more water to leak into the coal seam, displacing methane and pushing it to the surface.

But even when Amoco’s consultants acknowledged that the industry might be to blame for the leakage, there was no way to pin it on any well. And since no baseline data existed, there was no way to know that the leakage had increased. The uncertainty helped Amoco dodge litigation; when the homeowners sued the company, they lost. As time went by, and no more homes were contaminated and the price of natural gas crashed, the issue faded from the public consciousness.

Until now.

Eric Kort, an atmospheric scientist with the University of Michigan, is the lead author of last year’s hot-spot study, and on an April morning he is leading a forum on methane in Farmington. Some 200 people have crowded into a college room to hear scientists talk.

There’s a lot at stake. Shirley “Sug” McNall, a local who has been butting heads for years with the oil and gas industry over its impacts on air quality, is here, as are members of environmental groups, such as the San Juan Citizens Alliance and Western Environmental Law Center, are here. Officials from the two coal power plants west of town, which together with the coal mines employ hundreds of people, look on somberly. Most anxious, though, are the natural gas industry leaders.

The San Juan Basin is one of the nation’s most prolific gas fields, and as goes sentiment toward natural gas, so goes the fate of Farmington restaurants, schools and government. It appears these scientists hold that fate in their hands.

As the shale revolution yielded a natural gas glut and decreased prices, it chipped away at coal’s supremacy until April, when natural gas generated more electricity in the U.S. than coal. That same month, carbon dioxide emissions from the electric power sector reached a 27-year low, after steadily declining for the past several years. It was a big win for the climate. Or was it?

In 2011, Cornell University’s Robert Howarth dropped a bomb on the party when he suggested that natural gas may have a larger greenhouse gas footprint than coal, thanks to methane leakage. Though the study remains in dispute, it woke people up to the fact that the fuel has an Achilles’ heel. Methane has 86 times more global warming potential than carbon dioxide over a 20-year span, and up to 30 times over a century. That means that for every 100 tons of carbon dioxide kept out of the atmosphere, it only takes three or four tons of methane to offset the gain. Howarth concluded that in order for natural gas to retain its greenhouse gas superiority over coal, leakage rates had to stay below 2.8 percent.

EPA greenhouse gas inventory data show that the national leakage rate is about 1.5 percent, which sounds pretty good. But independent studies have found that actual emissions are often far higher than what is reported to the agency. Petron, for example, found that oil and gas production in the Denver-Julesburg Basin emitted three times more methane than the EPA inventory showed. And in 2014, Kort, Petron and others published a paper in Science documenting that, nationwide, measured emissions were 1.5 times higher than those in the inventory. Now they’re trying to see if the same is true in the Four Corners. To achieve concentrations like those found in this hot spot, says Kort, emissions would need to total about 590,000 metric tons per year. That’s 150,000 metric tons more than all the emitters in the region report to the EPA.

Kort had speculated that the increase could result from fugitive emissions that the companies don’t know about, like the apparent slow leak in the wellhead that showed up on Petron’s monitor, or perhaps from known emissions from facilities that fall below the inventory’s reporting threshold. Pipelines frequently rupture, releasing huge quantities of gas: A High Country News analysis of data from the Pipeline and Hazardous Materials Safety Administration revealed that ruptured pipes have leaked enough methane since 2010 to heat 170,000 homes for a year. Perhaps hundreds of abandoned gas and oil wells, leaking but unaccounted for, are to blame. If this is true, it could put the coalbed methane field’s leakage rate as high as 8 percent.

The industry disagrees. “The San Juan Basin is well-known as a large area of natural seepage – when methane emissions are naturally occurring and not the result of energy development,” writes Katie Brown for Energy In Depth, a PR outlet for the Independent Petroleum Association of America. Such claims, however, are “little more than a bogus, rhetorical diversion to avoid responsibility and to undermine ongoing rule-making efforts,” says Erik Schlenker-Goodrich, executive director of the Western Environmental Law Center.

At the forum, Kort, Petron and other scientists assure the audience that they will look at all potential sources, including geologic seeps. The scientists’ analysis won’t be published until next year, but research hints at what they might find. Monitored seeps along the Colorado side of the coal outcrop have leaked more than 45,000 metric tons of methane per year, which has the same warming potential as the carbon dioxide emitted from more than 200,000 cars annually. Still more methane is leaking from other parts of the outcrop that aren’t monitored, in New Mexico, or on the Southern Ute Reservation, where data has not been made public. The seeps are a significant source. But by its own count, ConocoPhillips’ San Juan Basin operations released six times that amount – 277,000 tons – in 2013, making it the largest emitter in the nation.

Also lingering is the question of how much of the seeps’ emissions can be attributed to the coalbed methane industry. A report published in 2000 as part of the multi-agency project to map, model and monitor the coal outcrop again established a link between drilling and the seeps, but some mystery remains. The researchers have found, for example, that the total emissions from the seeps in their monitoring zone has increased each year since 2007, yet no one is trying to determine why. It could be drought, it could be changes in the gas field, or it could be something else entirely. Hencmann hopes the attention on the hot spot will revive flagging efforts to decipher the seeps.

Without understanding the connection between anthropogenic and natural seeps, there’s no mechanism for encouraging companies to mitigate those seeps. Unless we know how much the industry is responsible for, we can’t calculate the leakage rate of the region’s natural gas systems and therefore can’t really know how big its greenhouse gas footprint is.

A new round of research could have global implications. Similar basins exist all over the world, says Taku Ide, a petroleum engineer who studied methane-fueled fires on Southern Ute land. The Intergovernmental Panel on Climate Change estimates that, worldwide, geologic seeps could be emitting as much as 40 to 60 million metric tons of methane per year, putting them on par with landfills or coal mines.

“The San Juan Basin is the most advanced in terms of work that’s been done to serve as a model, to drive the conversation across the U.S.,” says Ide. “It could be a model child.”

South of Farmington, white sandstone cliffs rise along the San Juan River. From these cliffs, you can look out over a landscape that is beautiful and battered, sacred and sacrificed. You can see the nation’s energy past, and perhaps its future.

To the west, two coal-burning power plants stand in the high desert. Each kicks out more than 11 million tons of carbon dioxide each year, along with particulates, sulfur dioxide and mercury. When the wind rises, a gray dust lifts up into the air from the piles of coal-combustion waste piled near the Four Corners plant.

Environmentalists and Navajo activists have struggled to shut down the plants. Four Corners recently shut down three of its five generators to comply with regional haze rules, and San Juan Generating Station plans to shut down two of four units and replace one with a natural gas-fired “peaker” plant unless opponents succeed in retiring the plant altogether.

The shutdowns have come in part with the help of the coalbed methane and conventional natural gas fields that pockmark thousands of square miles here. Much of the gas is piped to California to run power plants, thereby helping to wean themselves from the two coal plants here. President Obama’s Clean Power Plan, released this summer, will likely tilt the nation’s energy balance toward natural gas. That could do more to clean up this area’s coal-sullied air and landscape.

But it would also increase activity in the gas fields. More wells would provide more avenues for methane to escape, adding to the hot spot.

This summer, the EPA announced a program to get companies to clean up their act, and industry officials have promised to comply. ConocoPhillips says that it has reduced overall emissions by 48 percent on its own, but just 10 of New Mexico’s 475 natural gas producers participate in the EPA’s EnergySTAR program, and with natural gas prices so low, there’s little incentive to invest much into leak prevention. That’s why activists want the entire industry to tighten up.

In August, the EPA released its new rules requiring operators to plug leaks of methane and other toxics on new and modified facilities and capture the methane that burps out of any newly fractured oil or gas well. Since the rules don’t apply to existing infrastructure, they will do little to reduce the methane cloud. But the BLM will hand down its own rules in coming months, and they are expected to apply to these existing facilities. The majority of the wells in the San Juan Basin are under BLM jurisdiction, so the new rules should have an effect on the hot spot. Indeed, Interior Secretary Sally Jewell invoked the Four Corners hot spot when announcing the need for such rules in March.The BLM regulations may resemble Colorado’s, implemented last year, which require companies to install leak-detection and prevention equipment and take other measures to reduce emissions.

Chris Colclasure of the Colorado Air Pollution Control Division says it’s too soon to quantify the effects of the rules, but he believes they work and are not too onerous for the companies. In fact, several energy firms have endorsed the regulations, saying they’re good for business.

The scientists working to decipher the methane mystery remain mum when it comes to specific regulations, but they have discussed what they think needs to be done. “If natural gas is to be a ‘bridge’ to a more sustainable energy future,” wrote Kort, Petron and several other researchers in a paper published by Science last fall, “it is a bridge that must be traversed carefully: Diligence will be required to ensure that leakage rates are low enough to achieve sustainability goals.”

Back at the gas well behind the high school, Petron lets me flip the switch that snatches an air sample from the breeze. It will tell Petron and Thorley which isotopes of methane are here, and, which compounds may be seeping out of the well. Methane’s not going to hurt anyone in the short term unless it builds up enough to explode, but benzene, another pollutant emitted by oil and gas wells, has short- and long-term health effects and is a known carcinogen – certainly not something you want your high-schoolers inhaling every day.

As we pull back onto the road, Petron reminds me of one simple, enduring fact of life here in oil and gas country: “Your air is being impacted,” she says. “You live on the edge of the gas field.”