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Betsy Southerland knew something was wrong the moment she walked into her office at the Environmental Protection Agency.

It was 8 a.m. on a Thursday in April and already, her team was waiting at her door, computer printouts in hand.

For months, staffers in the Office of Water had been in help-desk mode, fielding calls from states implementing a federal rule that set new limits on water-borne pollution released by coal-fired power plants. The rule on what is known as "effluent" had been hammered out over a decade of scientific study and intense negotiations involving utility companies, White House officials and environmental advocates. The EPA had checked and rechecked its calculations to make sure the benefits of the proposed change outweighed the cost to the economy.

But now, members of Southerland's team were handing her a press release, firing questions as her eyes skimmed the page. 

Did she know about this? Had she seen it? What happened?

The announcement from EPA Administrator Scott Pruitt said the agency was considering undoing the rule. "This action is another example of EPA implementing President Trump's vision of being good stewards of our natural resources, while not developing regulations that hurt our economy and kill jobs," the release said.

Southerland was stunned. In three decades as a career staffer at the EPA, she'd never seen an administrator describe a regulation in such terms. As director of science and technology for the office, she also had never learned of such a major change of direction from a press release. She couldn't give her team any answers. "I was as clueless as they were," Southerland recalled.

 have been either opened for reconsideration or overturned altogether. These regulations would have had far-ranging effects, from banning hazardous pesticides and offshore oil drilling to stopping coal-mining debris from being dumped into local streams to forbidding hunters from shooting Alaskan wolves on wildlife refuges. They would have required infrastructure projects to be built to higher flood standards and greenhouse gas emissions to be limited and tracked.

ProPublica took a close look at the effluent rule, which was one of the most scrutinized and meticulously researched of the regulations the new EPA leadership is preparing to overturn. Longtime staffers and environmental experts say it is an instance in which science and prevailing industry practices were swept aside to benefit a handful of coal-fired power plants that were having trouble meeting the new standards.

A spokeswoman for the EPA said the change of direction is part of a broader push to eliminate unnecessary federal rules.

"Administrator Pruitt has made a commitment to refocus the Agency back to its core mission of protecting human health and the environment, restore power to the states through cooperative federalism, and improve processes by adhering to the rule of law," the spokeswoman told ProPublica. "This includes a review of regulations passed by the previous administration that may impose unwarranted burdens or exceed our statutory authority."

Many of the rules were years or even decades in the making, and the sheer speed with which they've been cast aside has left the EPA staffers who helped craft them shaken.

It has also deepened the chasm between the agency's top decision-maker and his agency's longtime staff. Pruitt's opposition to EPA regulation was a defining feature of his career before he took the agency's reins. As Oklahoma's attorney general, he sued the EPA repeatedly and blasted its rules as overreaching. Since taking the administrator post, it's been reported that he's given lobbyists broad access and appointed people to key jobs who have close ties to the industries they are overseeing.

To the Trump administration and its supporters, this is no more than a long overdue balancing of the scales. In any administration, one side is always happier than the other, said Fred Palmer, a senior fellow at the Heartland Institute, a free-market think tank. "They are not being listened to because they disagree with the agenda of the President of the United States who, at the end of the day, is their boss," he said of EPA staffers, "like it or not."

Pruitt's interaction with Southerland and her team on the effluent rule reflects the degree to which the EPA is now shutting its own staff out of the decision-making process.

Under previous administrations, Republican and Democratic alike, Southerland said staffers could make their case to agency leaders, presenting the scientific evidence behind rule-making proposals and other regulatory decisions. They didn't always win the day, but they often managed to hold onto the provisions they considered most important.

But under Pruitt, she and others said, EPA's career staffers have seen their access to the agency's leadership dwindle. More importantly, their arguments no longer have much influence on the rapid-fire series of decisions announced by Pruitt.

"This has been a long-planned assault on the agency, not some serendipitous thing," Southerland said. "(Staffers) now understand that the overall process will be to repeal everything requested by industry."

The long road to the revamped effluent rule began in 2005.

"Effluent" is wastewater that is allowed to be discharged into rivers and lakes, a byproduct of 59 different industries, from commercial animal farms and landfills to soap companies and dental offices. This wastewater often contains dangerous toxins.

The Clean Water Act — a bedrock environmental protection that sought to make American waters "fishable and swimmable" — requires the EPA to set limits on toxins found in effluent. The rules must be updated every five years to keep up with advances in the technology that filters out dangerous chemicals.

Within the EPA, this task belonged to the Office of Science and Technology, a team of more than 100 scientists, engineers and economists within the Office of Water who develop standards to protect water safety and recommend limits for levels of contaminants. To update the effluent limits, the team had to understand how much each industry was polluting the water, how each processed its waste and how that process was evolving.

But the sheer volume of effluent-generating industries made it impossible for the office to revise the rules every five years. So, the office set priorities.

Every year, the office reviewed pollutant discharges reported by companies and ranked them into categories that posed hazards to human health and the environment. In 2003, EPA's screen found that coal plants ranked high in discharges of toxins and pollutants.

To keep coal ash — the carcinogenic leftovers from burning coal — from winding up in the air, some power plants use what are called scrubbers to trap it. Those scrubbers need to be cleaned, and the residue is mixed with water and stored in ponds. To keep those ponds from overfilling, plants ultimately release effluent into nearby waterways. It's a potentially hazardous process. Effluent from coal ash contains mercury, arsenic, lead and selenium — elements linked to an increased risk of lower IQs in children, cancer and organ damage.

In the mid-'00s, when the EPA's concern about effluent from coal ash ponds grew, federal rules were silent on these toxins. The limits focused on curbing oil, gas and total suspended solids — the visible stuff floating in coal ash wastewater. The regulations hadn't been revised since 1982.

There was a growing body of studies and news reports detailing the damage caused by chemical contaminants from coal plant wastewater. Researchers learned of fish turning up deformed and dead, and bullfrogs found crippled, missing entire rows of teeth. There were reports about coal ash ponds leaking and contaminating nearby groundwater. Drinking wells were poisoned in Maryland and Indiana.

The office needed more data to form the basis of a new rule. It started collecting it in 2005.

First, staffers needed to understand what technologies companies were using to control pollution from coal plants, how much it cost and how clean the wastewater could get. They created a 391-page 

 that would ultimately reach 733 facilities.

In 2006, EPA scientists started visiting power plants to better understand how they operated. This launched eight years of study that took them to 73 facilities in 18 states. They collected samples to understand how different types of coal polluted the water and how well different treatment systems performed. Their investigation took them all the way to southern Italy, where a power plant in Brindisi was using an advanced wastewater evaporation process to protect an aquifer.

By 2009, the office reported their findings, saying it was clear newer technologies were available to "significantly reduce" the presence of harmful pollutants in public water, and that existing regulations were far out of date.

The office had the evidence it needed to move forward with stronger limits on coal plant effluent.

Even as the EPA prepared to move forward on a rule, environmentalists grew concerned about reports on coal ash wastewater. On top of that, the Obama administration was strengthening rules to keep coal plants from pumping toxins like mercury into the air. If the rule went through, coal plant scrubbers would capture even more toxins, much of which would eventually end up in coal ash ponds that would discharge effluent.

"You're taking the pollution out of the air and putting it into the water," said Jennifer Peters, national water programs director at Clean Water Action. "That triggered concern within EPA and the environmental community wanting to ensure that they're not just moving the pollution problem around."

Environmentalists prodded the EPA to look at the danger to both the air and the water, but officials were in the thick of revising other regulations. So in 2010, several environmental groups sued the agency to force it to get the new effluent rule out sooner.

In a consent decree, reached in November 2010, the EPA agreed to propose an updated effluent rule by 2012, with a final rule coming no later than 2014. But there was a complicating factor.

Another EPA branch — the Office of Land and Emergency Management — was drafting another rule about coal ash waste. Called the Coal Combustion Residuals rule, it was aimed at making sure coal ash ponds and landfills were structurally sound. The two rules needed to work in harmony, but scientists from each office had collected data in different ways. The data needed to be standardized, and distinct costs and benefits assigned to each rule. The benefits of each rule had to justify the costs — a Clinton-era reform designed to limit excessive regulation.

The task fell to the Office of Science and Technology, which Southerland had just taken over after leaving another branch of the EPA. The analysis took longer than expected.

"We kept asking for delays because we kept having to redo the analysis on both rules to make sure we weren't double counting the benefits," Southerland said.

By now, her office was confident in its research, which showed some companies were using biological and chemical processes to clean wastewater. These other processes drastically reduced the toxins that ended up in the water, as well as the amount of water that needed to be released.

Southerland's office crafted a rule that set limits on the amount of toxins that could be discharged. And though it didn't specifically forbid using coal ash ponds, the rule would have forced plants to use technologies that could meet the more stringent limits.

It was time to take the proposed rule to the next phase.

In January 2013, the EPA submitted it to the White House's Office of Information and Regulatory Affairs, a forum for other agencies to review pending regulations and for lobbyists to weigh in. OIRA is a gatekeeper for all federal rules and needs to give final approval for any rule.

The substance of OIRA meetings are confidential, but public logs show that utility industry lobbyists and lawyers had ample opportunity to make their case.

In the end, the Obama administration office approved coal ash ponds as the "best available technology," contrary to EPA's recommended option. OIRA also 

 of the scientific findings and softened language toward coal utilities while finding that the benefits of the rule were less than the EPA had projected.

When the proposed rule went out for public comment, utilities argued the EPA was underestimating its cost, that wastewater was already being addressed through other regulations and that there was no proof that newer technologies were more effective in reducing the concentration of toxins in wastewater. Environmentalists had their own complaints, pressing the agency to eliminate wastewater discharges entirely and arguing the proposed regulations would likely lead to new coal ash ponds.

In all, more than 200,000 members of the public weighed in during the four-month comment period, largely due to letter-writing campaigns from environmental groups. A California woman recounted how industrial coal processing chemicals fouled water in West Virginia, leaving her friends with unsafe water for weeks. A West Virginia woman pleaded for help: "One thing's for certain — our state oversight of this immense environmental legacy is sorely lacking and we desperately look to the EPA to stand up for us!"

Industry weighed in as well, often attaching voluminous studies and additional monitoring data to their comments. Southerland said she led the team in around-the-clock analyses to see if the industry-provided data affected the calculations that went into the rule.

At the same time, Southerland's boss mounted a campaign to push OIRA to approve EPA's original version of the rule.

Ken Kopocis, a lawyer who worked on Capitol Hill for more than 25 years before Obama nominated him to lead the Office of Water, said he appealed to "high-ranking" officials in the Office of Management and Budget, which oversees 

, and also the White House, walking them through the research.

"My people in Water didn't think we were going to be able to get the rule we wanted," Kopocis said. "I said, 'No, we're going to fight for it and we're going to get it.' ... OIRA is full of capable people. But they don't know as much as the agency does."

Kopocis' strategy worked: He was able to convince OIRA to reverse its initial decision.

The final rule, released on Sept. 30, 2015, substantially mirrored EPA's original proposal, setting strict limits, for the first time, on the amount of selenium, arsenic, mercury and nitrate utilities could discharge. It didn't prescribe a specific technology plants needed to use to achieve this goal, but it said the tougher limits couldn't easily be met using coal ash ponds.

This rule was "incredibly significant," Kopocis said, because there's "no dispute" that the toxins curbed by the rule are harmful. "It's just incredible that we had all of these pollutants being put into water bodies when the technology was available to stop it."

And it turned out, most utilities had already moved to comply with the toughened rule. EPA officials found that only 12 percent, about 134 facilities, needed to update their technology.

Officials knew some plant operators wouldn't be able to afford the upgrades. "There might have been a plant or two that would have ended up closing," Kopocis said.

The EPA gave utilities years to raise the money needed to limit the toxicity of the liquid they released. The rule required them to start cleaning up their discharges by November 2018 and until 2023 to complete the transition.

The rule was challenged in courts around the country. Industry lawsuits said it was too difficult to comply with the rule; environmentalist lawsuits said it needed to go further. For months, cases were in limbo as they were consolidated before a single court. Industry and environmentalists tried to compel the EPA to disclose confidential business information gathered to create the guidelines — data that could be picked apart to bolster their legal arguments. The EPA asked the court for time to prepare briefs, delaying the case to 2017.

All this was pretty much par for the course for any new EPA rule.

Inside the Office of Science and Technology, Southerland's team moved forward with implementing the rule, holding webinars, writing documents and answering state regulators' questions about how to put the guidelines into practice. They continued that work as the Obama administration ended and the Trump administration brought new leadership to the top of the agency.

Standing there on that April morning, press release in hand, Southerland didn't panic.

She had navigated setbacks under all kinds of administrations since she joined the EPA in 1984. Trained as an engineer, with a doctorate in environmental sciences and engineering, she said her instinct was to brief the administrator on the science.

She gathered key staffers around a conference table and got to work.

They quickly decided their old briefing documents from the Obama administration were too technical. For 90 minutes, they outlined the contours of four briefings — one each on how the rule came together, why it was affordable, why it was necessary, and the legal challenges that might arise from further revision.

Southerland told her team they needed to give Administrator Pruitt "all the relevant facts," she said, so he "could make a good decision." He was reconsidering the rule, but before he restarted the formal rulemaking process, they hoped they could persuade him not to throw it out completely.

These were their best arguments: The rule was already being widely followed by the industry. The industry claim that the rule would cause power plants to close was likely wrong — many plants lacking the appropriate technology were already slated for retirement, pushed out by the low cost of natural gas. The delayed compliance dates would give the remaining companies time to plan and pay for the shift.

The team spent the rest of the day fleshing out details.

"We were absolutely hopeful," Southerland said. "We thought if anything, we could talk him into repealing just a small part of it."

They tried to get on Pruitt's schedule, but he was booked — often with back-to-back speaking engagements, meetings and briefings with industry executives, published 

While they waited to meet with Pruitt, Southerland and her team worked on those around him. For two months, they held in-person and phone briefings with EPA lawyers, high-ranking political appointees and career staffers. In meeting after meeting, they walked different officials through the development of the rule, the legal issues related to it, and the price tag for implementing it. They received no pushback from Pruitt's lieutenants in those briefings, staffers said, and few questions.

Finally, they had two briefings on July 14 and July 21 with Pruitt himself, packing all of their talking points into those one-hour time slots.

Walking into the administrator's packed conference room for the first time, their hopes were high. "We assumed we had dazzled them and this was just the finishing touch," Southerland said.

In the first briefing, the team explained how it developed the rule and calculated its costs; then, it laid out the arguments industry had raised and, point-by-point, gave potential options for solving them.

Pruitt took notes and was "attentive," Southerland said, but asked few questions.

In the second briefing, the team laid out the bottom line of Pruitt's options and the consequences of each. Reopening portions of the rule would likely mean even more stringent effluent limits down the road, since technology had improved since the final rule was released in 2015, they said. Repealing the entire rule would rollback all of the protections — even those that utilities supported.

Finally, Pruitt asked if there was anything else the staff wanted to say. Staffers added that municipal water utilities had expressed concern that, without the rule, they would bear the costs of keeping effluent pollutants out of the drinking water supply. Staffers also noted that putting the rule on hold would lead to confusion for states renewing discharge permits for coal plants. When the staffers finished speaking, Pruitt thanked them. The meeting was over.

On the walk to the elevator, the team was ecstatic.

"We thought we made all of our points and that we couldn't have done a better job explaining how important and affordable this rule was," Southerland said.

The EPA now had to hear from the public. In May, Pruitt had proposed delaying the deadline for coal plants to comply with the effluent guidelines while the agency considered whether to revise the rule entirely. The proposed rule triggered a public comment period, including a hearing on July 31 in which 71 people signed up to testify. Only three speakers were from industry. The rest begged for the effluent limits to remain intact.

"If somebody backed a tractor trailer truck of mercury up to my lawn or your lawn and dumped it on your lawn, what would you do?" said environmental attorney Robert F. Kennedy Jr. "You would say to them, 'Clean it up. Clean it all up.' And if they said to you, 'Well, it's too costly for us to do that,' you would say, 'I don't care what the cost is. You have no right to do that, ever.'"

 to lobbying groups that had requested that the rule be reopened, announcing that the EPA would re-examine the pollution limits that the new effluent rule set for the two biggest sources of wastewater from coal plants, potentially erasing the thrust of the rule issued in 2015.

Not long after, Pruitt's office announced that "substantive portions" of the other rule to regulate coal ash ponds, the Coal Combustion Residuals rule, would be reconsidered. An EPA spokeswoman said "there were significant issues" with both rules that "justify the need to take a second look."

"We were heartbroken," Southerland said. "We raked ourselves over the coals trying to say 'what more could we have done?'"

The reopened effluent rule sent ripples through the coal plant industry and beyond.

In Indiana, a company that planned to install $400 million in upgrades 

 seeking funding for a system that would have complied with the new pollution limits. The company, Northern Indiana Public Service Co., will "revisit... investments once the EPA completes its review," said director of external communications Nick Meyer.

federally owned independent power company

 — told state regulators it was holding off on installing new technology until 2023. The company said it was awaiting guidance from the state, which was waiting for the EPA. "We're not delaying anything," Scott Brooks, the company's spokesman, said, "but when you have a rule that's suspended, you go back to what was in place prior to the guidelines that were suspended."

Frontier Water Systems, which had created a 

 for dry-handling coal ash waste, is already feeling the squeeze. The company has about 24 employees in San Diego, Salt Lake City and outside of Atlanta and is on track to do $15 million in business this year. But the company's future is uncertain, since so much relies on when or if coal plants will be required to clean up their waste streams. One of the owners, Jamie Peters, said they'd consider selling their technology to China or another country if it's unsustainable here.

"If this rule is delayed significantly or removed, we would probably have to abandon this," Peters said. "I don't think we have years; we have months."

The new rulemaking process could take a few years, former officials said, since the EPA will have to collect data about the current state of wastewater technology in order to propose a replacement standard, then go through the interagency review process again and allow for more public comments.

Now, Southerland is on the outside looking in. In an interview with ProPublica, Southerland, 68, said she opted to retire in August for family reasons, though she's been an outspoken critic of Pruitt since she left.

She made her farewell letter public, and it went viral.

"The truth is, there is NO war on coal, there is NO economic crisis caused by environmental protection, and climate change IS caused by man's activities," she wrote.

At her retirement party, she read the speech to the colleagues she was leaving behind — the ones tasked with orchestrating repeals of rules they crafted. Her scathing critique was both an acknowledgement of their current reality, and a plea to stay the course.

"I know in my heart that the majority of Americans in this country recognize that protection of public health and safety is a right and it is just," she said. "And so this will happen. And all of you must just wait for that day to come — whether it's two years, three years or four years: that day will come. So, do not give up. Do not feel that your efforts are going to go to waste in these four years. Because, eventually, you will overcome."

At first, Southerland said, scientists at the agency expressed optimism that they could prevent rules they'd spent their careers to advance from being weakened or scrapped. But as time wears on, she said, that hope is fading.

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