Gary Rinehart clearly remembers the summer day in 2002 when the stranger walked in and issued his threat. Rinehart was behind the counter of the Square Deal, his “old-time country store,” as he calls it, on the fading town square of Eagleville, Missouri, a tiny farm community 100 miles north of Kansas City.

The Square Deal is a fixture in Eagleville, a place where farmers and townspeople can go for lightbulbs, greeting cards, hunting gear, ice cream, aspirin, and dozens of other small items without having to drive to a big-box store in Bethany, the county seat, 15 miles down Interstate 35.

Everyone knows Rinehart, who was born and raised in the area and runs one of Eagleville’s few surviving businesses. The stranger came up to the counter and asked for him by name.

“Well, that’s me,” said Rinehart.

As Rinehart would recall, the man began verbally attacking him, saying he had proof that Rinehart had planted Monsanto’s genetically modified (G.M.) soybeans in violation of the company’s patent. Better come clean and settle with Monsanto, Rinehart says the man told him—or face the consequences.

Rinehart was incredulous, listening to the words as puzzled customers and employees looked on. Like many others in rural America, Rinehart knew of Monsanto’s fierce reputation for enforcing its patents and suing anyone who allegedly violated them. But Rinehart wasn’t a farmer. He wasn’t a seed dealer. He hadn’t planted any seeds or sold any seeds. He owned a small—a really small—country store in a town of 350 people. He was angry that somebody could just barge into the store and embarrass him in front of everyone. “It made me and my business look bad,” he says. Rinehart says he told the intruder, “You got the wrong guy.”

When the stranger persisted, Rinehart showed him the door. On the way out the man kept making threats. Rinehart says he can’t remember the exact words, but they were to the effect of: “Monsanto is big. You can’t win. We will get you. You will pay.”

Scenes like this are playing out in many parts of rural America these days as Monsanto goes after farmers, farmers’ co-ops, seed dealers—anyone it suspects may have infringed its patents of genetically modified seeds. As interviews and reams of court documents reveal, Monsanto relies on a shadowy army of private investigators and agents in the American heartland to strike fear into farm country. They fan out into fields and farm towns, where they secretly videotape and photograph farmers, store owners, and co-ops; infiltrate community meetings; and gather information from informants about farming activities. Farmers say that some Monsanto agents pretend to be surveyors. Others confront farmers on their land and try to pressure them to sign papers giving Monsanto access to their private records. Farmers call them the “seed police” and use words such as “Gestapo” and “Mafia” to describe their tactics.

When asked about these practices, Monsanto declined to comment specifically, other than to say that the company is simply protecting its patents. “Monsanto spends more than $2 million a day in research to identify, test, develop and bring to market innovative new seeds and technologies that benefit farmers,” Monsanto spokesman Darren Wallis wrote in an e-mailed letter to Vanity Fair. “One tool in protecting this investment is patenting our discoveries and, if necessary, legally defending those patents against those who might choose to infringe upon them.” Wallis said that, while the vast majority of farmers and seed dealers follow the licensing agreements, “a tiny fraction” do not, and that Monsanto is obligated to those who do abide by its rules to enforce its patent rights on those who “reap the benefits of the technology without paying for its use.” He said only a small number of cases ever go to trial.