An imprisoned grad student tests our alliance with India.

In December 2005, a Purdue graduate student named Vikram Buddhi began posting a series of ugly notes—“Kill GW Bush,” “Rape And Kill Laura Bush,” “Kill Donald Rumsfeld The Old Geezer Crook”—on a message board devoted to technology. A few months later, Buddhi, an Indian citizen who was in the United States to study math, was arrested and charged with threatening the life of the president—a federal crime. He was convicted in June 2007 and, this past December, sentenced to nearly five years in prison.

I had never heard of Buddhi until a recent trip to India, but his story has attracted attention there. Many of the country’s major newspapers have carried investigative stories about the case, as has NDTV, one of India’s largest TV stations. In 2009, after the channel aired an interview with Buddhi from prison in Chicago, the reporter signed off by saying that Buddhi’s “American dream had become a nightmare.” Shortly after Buddhi’s sentencing, ten protesters hurled rolled-up flyers at the U.S. consul general in Mumbai during a press conference. Buddhi’s imprisonment, the flyers said, was a “warning to all Indian youth who are committed to redeeming their land from the forces of U.S. imperialism.”

Leading the charge on behalf of Buddhi has been his father, Buddhi Subbarao, a prominent gadfly who is revered within certain quarters of the Indian elite for his willingness to question the government, and who was an outspoken opponent of the recent nuclear deal between India and the United States. When I met him last month in the lobby of the Taj Mahal Hotel in Mumbai, he spun an elaborate theory about the case. The U.S. Secret Service, he said, concluded that his son posed no serious threat when it initially investigated him in early 2006. But, between the time of that investigation and his son’s arrest in April, Subbarao published a technical article criticizing the nuclear deal. “On what basis was he arrested on April 14?” Subbarao asks me. “Is there a new development? The only new development is an article written by me.”

There is no evidence to support Subbarao’s claim; and, while plenty of Indians seem to believe that Buddhi was treated unfairly by the U.S. justice system, I doubt many share his father’s darkly conspiratorial view of the case. Moreover, the Buddhi saga was hardly an earth-shattering development in U.S.India relations. Still, the entire episode is a reminder that Indians’ feelings about the United States are somewhat more complex than we often assume. Americans tend to think of India as a natural ally. The two countries share a common language (English), a common enemy (jihadism), a common rival (China), and a strong trade relationship. And, on the surface at least, the United States is well-liked in India. In 2009, the Pew Research Center found that 76 percent of Indians viewed the United States favorably—making it more popular in India than in Canada, Britain, or Israel.

Yet, for all these outward signs of comity, the relationship is not without its share of friction. These days, much of that friction traces to the nuclear deal that so exorcised Buddhi’s father. The agreement—which offered India cooperation on civil nuclear power but would likely be imperiled if the country ever conducted another nuclear weapons test—was seen by many nonproliferation advocates in the United States as overly generous to India, since it extended benefits to a nation that had never signed the Nuclear Nonproliferation Treaty. But, in India, the deal was viewed by its many critics as a blow to national pride. It was opposed not just by the country’s nuclear establishment and the major conservative opposition party, but also by some of the left-leaning parties that made up the governing coalition of the prime minister, Manmohan Singh. (The controversy surrounding the deal sparked a no-confidence vote in India’s parliament, which Singh barely survived.)

Teresita Schaffer, author of India and the United States in the 21st Century and director of the South Asia Program at the Center for Strategic and International Studies, traces this opposition to a tradition of “strategic autonomy” in Indian foreign policy. During the cold war, India was the leader of the nonaligned movement; now, Schaffer explains, many Indian elites continue to believe that India should “not allow powerful countries to influence its foreign policy.” The Times of India’s Mumbai bureau chief, Subramani Balakrishnan, put it this way last month, to a small group of reporters (we were all in India on a trip sponsored by the East-West Center): The nuclear deal, he said, “has the effect of tying India to a chair.”

Washington’s close relationship with Pakistan is also a source of irritation for much of India’s political class. While the left has historically worried about U.S. imperialism, says C. Raja Mohan, the strategic affairs editor of the Indian Express (and a supporter of the nuclear deal), the right has generally worried about Washington’s support for Pakistan and, beginning in the 1970s, its ties to China. “Historically in India there is deep distrust of the United States, both on the left and the right,” he says.

All this tension is not without practical consequences. Singh is currently taking heat at home from the right-wing Hindu nationalist opposition for bowing to U.S. pressure by considering renewed talks with Pakistan over the status of Kashmir. Meanwhile, Washington needs India’s help if economic sanctions against Iran are to work, but so far, that help has not been forthcoming. “We don’t think sanctions really achieve their objective,” Singh said at the recent nuclear summit in Washington. At a broader level, the United States needs India to be a stable cornerstone of an international system that can fight terrorism, proliferation, and other transnational threats. If Indian elites believe the United States is out to manipulate its sovereignty or aid its chief enemy, Pakistan, this will undoubtedly lead to problems down the road.

Paul Folmsbee, the U.S. consul general in Mumbai who was harassed by pro-Buddhi protesters at a press conference, is optimistic for the long term. “On the margins, there is friction,” he says. “But we are locked into a good relationship because we have shared values.” And that is mostly true. Except every once in a while, when a nuclear deal or an imprisoned grad student reminds everyone that the picture is a bit more complicated.

Eli Lake is a contributing editor of The New Republic.

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