WASHINGTON -- The long, strange story of Charles Monnett, a wildlife biologist who spent 14 years working in Alaska for the Department of Interior, is finally over. But it hasn't gotten any less strange.

Monnett announced this week that he had reached a settlement in the whistleblower case he had filed against the Department of Interior's Bureau of Ocean Energy Management (BOEM). Under the agreement, Monnett retired and received $100,000 and a conservation award that had been previously denied to him. His retirement became official on Nov. 15, and the agreement stipulates that he cannot apply for any other jobs with the department for five years. The settlement comes after a perplexing agency investigation into Monnett, who is best known for his 2006 paper on dead polar bears in the Alaskan Arctic.

Monnett said he's relieved to have reached a settlement over a "witch hunt" that had dragged on for nearly three years. "It's a relief to have it behind me, I guess," he told The Huffington Post.

The biologist's story starts back in February 2011, when a criminal investigator from the Department of Interior's Office of the Inspector General requested an interview. That interview focused largely on the paper Monnett published in the scientific journal Polar Biology in 2006, which described his observation of four dead polar bears floating in the Beaufort Sea during the annual whale survey two years earlier. Monnett and his coauthor predicted in the paper that declining sea ice would cause an increase in bear deaths. It was the first paper to document dead polar bears under those circumstances, and his argument attracted a good deal of attention for its inferences about climate change.

Five years after the paper's publication, in 2011, the IG's investigator wanted to talk to Monnett about it. And not just any investigator -- the IG's criminal investigator. But what exactly he was investigating was unclear. A transcript of the interview didn't make the point of the investigation any more apparent.

In July 2011, Monnett was put on administrative leave from the agency pending the results of the investigation. A spokesperson for the agency said at the time that it had "nothing to do with scientific integrity" or the paper. Instead, they said it was about unspecified "integrity issues."

Details released a few weeks later made it sound like the investigation's focus had shifted to the procurement process for a research project related to polar bears. The documents also stated that the matter had been referred to the Department of Justice, but that the DOJ "declined criminal prosecution." The Interior Department's investigator was still continuing its inquiry, however.

When the IG's office finally issued its report on the matter in October 2012, its only concrete allegations were that Monnett had leaked some emails about a 2007 environmental review of Shell's exploratory drilling plan for the Arctic -- a leak that DOI had been aware of since shortly after it happened. The agency issued a letter of reprimand in 2012 regarding the improper release of government documents and indicated it would take no further action.

"It was very confusing for a long time. It started out with the polar bear thing. That seemed like kind of a red herring," said Monnett. "Then it switched to the contracting thing. Then that fell apart. Then it became the release of information."

"As it played out, it didn't get better, it got worse," he said. "It just got crazier and crazier."

Monnett has been an official BOEM employee throughout this time, but he has been unable to do his work, which included managing tens of millions of dollars in research grants. "I haven't done much for a long time, because there wasn't anything that the agency really wanted me to do, apparently," he said. "Very little, other than busy work."

He filed a whistleblower complaint against the agency last January, alleging that the agency had effectively blocked him from doing his job. Public Employees for Environmental Responsibility has represented Monnett throughout the investigation and complaint. PEER announced Wednesday that Monnett had reached a settlement with the agency.

"They seemed pretty dedicated to trying to silence me, getting me out of the business of identifying studies to be done, and launching studies that were useful to understanding oil and gas development in the Arctic," said Monnett. "That was accomplished. They haven't silenced me, but they got me out of the business of doing studies."

Monnett described the last few years as "hell" for him and his family. Climate change deniers seized on the investigation, dubbing it "PolarBearGate." Deniers also went after Monnett's wife, a biologist who had previously worked for BOEM on endangered species issues, posting her email address online and urging people to contact her. Monnett said there had also been attempts to hack his email and computer.

Throughout the ordeal, Monnett and his representative at PEER have maintained that BOEM was caving to the oil and gas industry, which wanted to cut off Monnett's work on polar bears and other species. The investigation came at a time when the Interior Department was considering whether to add polar bears to the endangered species list, and as BOEM was reviewing Shell's plans to drill in the Arctic, a contentious issue. (BOEM was known previously as the Minerals Management Service, or MMS, until May 2010, when the agency was split up and renamed following the BP oil spill.)

Monnett says his managers were under "considerable pressure from the oil and gas industry," which was critical of his research. While many of his scientific colleagues left during the Bush administration, Monnett said, he "held on quite a bit longer."

"I was being effective," he said. "I felt compelled to work deliberately to get those studies in place. As long as the agency was supporting my program, then I felt pretty useful."

But that changed after the investigation started -- which Monnett says came as a surprise, given that President Barack Obama came into office pledging to do better when it came to scientific integrity and transparency.

"You'd like to think that, given what had been said at the beginning of the administration about science and transparency," Monnett said. "Then here I am, singled out for punishment because I was transparent and showed great integrity." He worries that the incident might have a chilling effect on other scientists in government agencies, he said.

Connie Gillette, a spokeswoman for BOEM, said that she could not comment on personnel matters. But in a statement she said that "[s]ound science is the foundation of BOEM's decision-making, and therefore we take the integrity of our scientists and the reliability of their work very seriously. We are proud of the exceptional scientists at BOEM and of BOEM's scientific programs."

Monnett says he's going to take some time off to spend with his family before looking for other opportunities. "Sixty-five is not that old. I think I can still play a useful role in some capacity," he said, but "clearly not in the Department of Interior."