“Everybody knew what to expect in Round 2,” Mr. Barrett said. “They would try to sell their best assets and leave their biggest environmental problems behind.”

Knack for Deals

The Natural Bridge is a rocky arch towering 215 feet above a small creek in southwestern Virginia.

Thomas Jefferson bought the property from King George III of England for 20 shillings. Today, it is owned by a nonprofit company started by Mr. Clarke. He bought the bridge in 2014, using a $9.1 million loan from the State of Virginia.

Mr. Clarke planned to revitalize flagging ticket sales to the bridge, then hand over the property as a state park. But his plans ran into trouble early on. Visitors dwindled, and he defaulted on his state loan. He had to use proceeds from selling coal and land to help get caught up on his bills.

In September, Mr. Clarke handed over management of Natural Bridge to the state. His nonprofit group, called the Virginia Conservation Legacy Fund, will still own the property until it pays back the loan. Some state officials praised Mr. Clarke’s work preserving the property but also had to give him more time to pay back his debt.

Mr. Clarke compares his struggles to those of the former president, who also ran into financial trouble at one point. “I sort of felt like I am having my Jeffersonian moment,” Mr. Clarke said.

Relentlessly upbeat, with a near permanent smile and the soothing voice of a public radio announcer, Mr. Clarke has spent a career trying to turn around an eclectic assortment of companies. He has bought troubled nursing homes, a forest preserve in Belize and a restaurant in Roanoke, Va. — a “philanthropub” that was supposed to dedicate its profit to Africa until it closed down in March 2015.

In the 1990s, he turned one of his companies, Lenox Healthcare, into a $400-million-a-year business — one of the largest nursing home chains in the country. His former business partner at Lenox, Lawrence B. Cummings, called him a master at bolting together impossible business transactions. “He showed again and again an ability to put together deals that other people couldn’t.”

Lenox was a juggernaut, Mr. Clarke said, until it went bankrupt in 1999. Mr. Clarke said he began to rethink his life’s goals. He went hiking in South America, where he met his wife, Ana, a native of Venezuela.

They moved to Virginia, converted his remaining nursing homes to nonprofits and placed them under a new company, Kissito (pronounced kiss-E-tow) Healthcare. He became interested in poverty issues in Africa and began raising money and building a maternity hospital in Ethiopia.

Mr. Clarke said he realized that many of the problems like drought and extreme floods in Africa were caused by climate change. Back in Virginia, Mr. Clarke said, he decided to take aim at the coal industry’s contribution to carbon emissions.

Too often, Mr. Clarke said, the debate over the future of coal is infected with what he called tribalism — a conviction that you are either with the mining industry, or against it. He said he was trying to find some middle ground.

Mr. Clarke’s first foray into the coal industry came when he took a job in late 2014 with Jim Justice, a wealthy West Virginia businessman who had built a fortune partly on coal. Mr. Clarke’s job was to assist Mr. Justice and his Southern Coal Corporation in dealing with hundreds of environmental violations at mines across Appalachia.

While results are difficult to track, some environmental groups acknowledge that Mr. Clarke’s work had an appreciable impact on the Justice properties. A Democrat, Mr. Justice is running to become West Virginia’s next governor. Through a spokesman, he declined to comment.

One of Mr. Clarke’s believers is Chandler Van Voorhis, a founder of C2I, a company outside Washington. C2I’s business is planting trees. The trees soak up carbon dioxide, converting it to wood and leaves. An acre of trees can convert 156 tons of carbon in one year, Mr. Van Voorhis said.


Mark Bartkoski, a miner, underground at the Federal mine No. 2 near Fairview, W.Va. Credit Luke Sharrett for The New York Times

C2I plans to reforest a million acres in the southern Mississippi River Valley and sell the carbon offsets to companies to reach pollution-reduction goals. Together, Mr. Clarke and Mr. Van Voorhis sketched a plan to bundle C2I’s carbon offsets with coal.

Their plan faced some steep challenges including this one: There was no natural market for coal bundled with pollution credits because of its higher cost.

Undaunted, Mr. Clarke hired an investment banker and lawyers to hatch his idea.

“Wall Street’s a pretty cynical place,” said Tim Hess, a real estate developer in Virginia, who introduced Mr. Clarke to his banking contacts. “But when you see somebody with that kind of passion and integrity, if there’s a way to make business sense out of it, I think people lean forward.”

A Reclamation Plan

Patriot Coal’s executives and advisers first met Mr. Clarke around the start of the company’s second bankruptcy case in May 2015.

For this second bankruptcy filing, Patriot chose to file in Richmond, Va., where restructuring experts say some judges are eager to move large bankruptcy cases through quickly. The choice turned out to be a fortunate one.

During the first day of bankruptcy hearings, Mr. Clarke said he happened to be in Richmond for a meeting with state officials when he wandered over to the federal courthouse. “It just amazed me how quickly they rushed through everything,” Mr. Clarke recalled of the proceedings.

The best mines would be sold to Blackhawk Mining, a coal company in Kentucky, which would run the properties with financing from some of Patriot’s lenders. The less valuable mines would be placed in a separate “liquidating trust.” The sole purpose of that trust would be to clean up water pollution and reclaim the mines.

West Virginia officials felt comfortable with this arrangement because they could pressure Patriot’s hedge fund lenders to contribute money to the trust for reclamation work, said Mr. Barrett, the lawyer for West Virginia’s environmental protection agency. Equally important, regulators could hold Patriot’s top executives liable for completing the mine cleanup. If they failed, the government could deny them mining permits until the work was completed.

“It was incredibly important to them personally, because these liabilities would follow them,” Mr. Barrett said.

But Mr. Clarke was proposing something else entirely. His nonprofit company would assume Patriot’s environmental and reclamation obligations. And ultimately, the deal would release former executives from liability.

At first, regulators and advisers to Patriot didn’t know what to make of Mr. Clarke. He had no experience. He had no traditional bank financing. When he came to meet Patriot’s management for the first time, he brought his young daughter with him. A company secretary watched her while he met with the executives for hours at the Charleston airport.

Many people involved in the negotiations assumed that Mr. Clarke had the financial backing of Mr. Justice, but that wasn’t the case.

Initially, state regulators did not consider Mr. Clarke a realistic option. So when Patriot signaled last summer that it was going to make a deal with Mr. Clarke, Mr. Barrett said, “we were floored.”

Shortly before a crucial court hearing, a major piece of Mr. Clarke’s financing fell through. Patriot’s lawyer and investment bankers scrambled to keep the deal from falling apart.


Supporters of Jim Justice, a wealthy West Virginia businessman who won the Democratic primary for governor this year. Tom Clarke got his start helping Mr. Justice and his company deal with hundreds of environmental violations. Credit Erica Yoon for The New York Times

In the end, Patriot agreed to effectively lend Mr. Clarke $5 million, and the coal miners’ union also stepped in with money. Surety companies that had insured Patriot’s reclamation obligations agreed to release millions in cash so Mr. Clarke could start the work.

Regulators and environmental groups worried that if the state held up the deal, Patriot could threaten to liquidate its properties, leaving no money for reclamations.

“It was the least bad outcome,” Mr. Morgan of the Sierra Club said.

Even if Mr. Clarke’s venture proves short-lived, Mr. Morgan said, he has already completed a good deal of reclamation work. Mr. Clarke said his fund has spent about $28 million on the work to date.

As insurance, Patriot’s lenders contributed $12.5 million to backstop the reclamation work in case Mr. Clarke failed. The state also has some control over the account that Mr. Clarke uses to pay for reclamation work.

For Mr. Clarke, the Patriot agreement opened the door to other deals. He took over reclamation obligations from Walter Energy, another mining company that had declared bankruptcy. He also picked up more viable mines and a coke processing plant from Walter. This spring, his company vied to take over an entire coal company, Alpha Natural Resources, but the bid was not accepted in the bankruptcy case.

“For someone with zero experience to come into this complex and troubled industry proposing the sort of things he is proposing is astonishing,” said Mr. McGinley, the law professor. “I give him the benefit of the doubt. But I don’t see where it is going.”

‘Coal Isn’t the Villain’

It was raining when Mr. Clarke and a clutch of miners rode a cavernous elevator 734 feet down to the dank shafts of Federal mine No. 2 last spring. At the bottom, the men boarded trains that clanked and jerked along wooden tracks through a maze of silent tunnels, empty except for the occasional mouse scurrying. The trains passed emergency shelters and ventilation shafts pumping cool air from above.

This is the miners’ 45-minute commute to the coal seam, where they shave off thousands of tons of black rock each week.

“I am proud of you,” Mr. Clarke told some of the miners.

As part of the deal with Patriot, the coal miners’ union invested $10 million and took a 20 percent stake in the Federal mine, which Mr. Clarke says he is doing everything he can to keep open even though it doesn’t break even.

When he bought the Federal mine from Patriot, Mr. Clarke said he expected to sell its coal for at least $50 a ton. Recent shipments have sold for just above $40 a ton, he said. On some weeks, the mine has had to operate on a three-day schedule because of the low demand for thermal coal, which is used to produce electric power.

Phil Smith, a spokesman for the United Mine Workers of America, said the union expected production to improve at the mine when the broader coal market recovered.

Still, Mr. Clarke’s company has shifted away from thermal coal and is hunting for mines that produce the much more valuable metallurgical coal used in steel production. Last month, an ERP-affiliated company acquired a set of huge surface mines in British Columbia out of bankruptcy.

Unlike many of the Patriot mines that Mr. Clarke acquired to clean up, these new mines are capable of pumping millions of tons of new coal onto the market each year and he’s projecting big profits next year.

Ultimately, Mr. Clarke hopes to offset all of the expected emissions from the coal he is producing with pollution credits. But right now, he is offsetting only 10 percent. That worries environmentalists. “It’s all I can afford,” he said.

Mr. Clarke says he has been absorbing the costs personally until he can persuade utilities and steel mills to agree to pay for credits. He is hoping that states, led by West Virginia, will allow utilities to pass through the costs of his credits to ratepayers. Those discussions are continuing, he said.

“Coal isn’t the villain,” he said. “The villain is excess carbon dioxide in the atmosphere, and we have to find ways to deal with it.”

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