NEW DELHI — FBI director Christopher Wray is in India this week for a trip aimed at strengthening security cooperation and deepening a partnership. But it comes in the wake of a major law enforcement issue between the two nations – one far more sinister and with the potential to cause cracks within that alliance.

Just two weeks ago, the United States accused an Indian government official of being involved in a conspiracy to kill an American citizen on its home soil.

The citizen in question is Gurpatwant Singh Pannun, a Sikh separatist, who was allegedly the target of a murder-for-hire plot in New York City.

Pannun is a wanted man in India – considered by the government there as a terrorist and national security threat. But to some Sikhs overseas, Pannun is an outspoken activist and a man rallying for a cause that has come to unite large swaths of the community’s international diaspora.

Late last month, US federal prosecutors charged an Indian national on suspicion of trying to kill him, according to an explosive indictment, which alleged the hitman was acting upon orders from an unnamed Indian government official.

The stunning revelation came little more than a month after Canada’s Prime Minister Justin Trudeau publicly alleged that India may have been involved in the murder of another Sikh separatist, Hardeep Singh Nijjar, on its soil, prompting a furious response from New Delhi and provoking a diplomatic fallout between the two countries. India has vehemently denied involvement in Nijjar’s murder.

The US plot was foiled and the details in the indictment have yet to be heard in court.

But the episode has cast “a dark shadow on New Delhi’s credibility,” wrote Suhasini Haider, the diplomatic affairs editor at The Hindu newspaper, in one of her recent editorials.

India’s government has denied any involvement in the alleged plot to kill Pannun. But in contrast to the vocal condemnation it made after Canada’s accusation, it has set up a high-level committee to investigate the accusations in the US indictment.

“As regards the case against an individual that has been filed in a US court, allegedly linking him to an Indian official, this is a matter of concern,” India’s foreign ministry said after the indictment was revealed.

The cause Pannun has been campaigning for is the creation of a separate Sikh homeland – one that would be known as Khalistan and include the state of Punjab in India.

Khalistan has long been outlawed in the world’s largest democracy, where painful memories of a deadly insurgency by some Sikh separatists continue to haunt many Indian citizens. But it garners a level of sympathy among some in the Sikh diaspora overseas, where protected by free speech laws, people like Pannun are able to openly advocate for secession from India.

The topic is highly charged. Four decades ago India’s former prime minister Indira Gandhi was assassinated by her Sikh bodyguards after she sent army troops charging inside the religion’s holiest shrine to flush out separatists that had been harboring inside. That operation, known as Blue Star, destroyed much of the building and left hundreds dead.

Riots broke out in the days after Gandhi’s murder, killing some 3,000 people – predominantly Sikhs – according to official figures, in one of the worst outbreaks of communal violence since India’s partition.

In the years since, those pursuing the Khalistan cause have formed a minority in Punjab given the government’s banning of the movement – and linked extremism doesn’t pose a significant threat to the country, analysts say.

But seeking reconciliation for what they view as human rights abuses committed against their community, several overseas Sikh organizations continue to advocate for Punjab secession and say the Khalistan movement is being falsely equated with terrorism by the Indian government.

Despite this, the government’s response to campaigners overseas remains robust, particularly under current Prime Minister Narendra Modi.

“India went through a very difficult phase with the Khalistan movement in 1980s. It defined their national security,” said Harsh Pant, vice-president of the Observer Research Foundation, a New Delhi think tank. “Therefore, the Indian state tends to take a very serious view of these things.”

Pannun, the Sikh separatist wanted by the Indian government, was a close associate of Nijjar, who was also wanted by India for terrorism related offenses.

A fiery orator Pannun has repeatedly made comments that are perceived as secessionist and threatening toward India and its government.

He is wanted on more than a dozen terrorism charges in India and accused of trying to radlicalize his community in support of the creation of Khalistan – an independent Sikh homeland that would include parts of India. India has outlawed the US-based secessionist group, Sikhs for Justice, headed by Pannun, which holds referendums among diaspora groups in support of Khalistan.

In a widely circulated video last month, he warned Sikhs not to fly Air India on November 19, citing “danger” to their lives. Headlines reverberated across India in the days that followed claiming Pannun was threatening to “blow up” the aircraft.

Pannun told CNN he was “not surprised” by the indictment outlining the foiled plot to kill him.

“The government of India has officially declared a reward on (my) head for running the global Khalistan Referendum campaign,” he said, referring to votes the Sikh diaspora around the world have held on gathering support for a separate homeland.

Asked by CNN if we was a threat to India, as New Delhi claims, he replied: “While my advocacy surely challenges India’s territorial integrity... this challenge is through ballots and not bullets, hence the challenge I pose is not considered terrorism under UN and international laws.”

On his remarks about Air India, he said comments in the Indian media were often misrepresented.

“My video message is to ‘boycott’ Air India not ‘bomb’,” he said. “This is a disinformation tactic of India’s Modi government to equate a non-violent call of ‘boycott’ with terrorism.”

Analysts say Pannun’s inflammatory rhetoric – and the media hype that surrounds him in India – could provoke backlash from citizens and prompt a government response.

“When you have someone making these statements regularly and Indian media broadcasting them, it takes the conversation beyond the confines of diplomacy,” Pant said. “Many Indians might ask why the US government is tolerating such behavior. The public perception of the danger may be much higher than the danger itself.”

To some, the Indian government’s alleged pursuit of an American citizen on its home soil might appear risky and put a dent in relations between two countries that have recently rapidly strengthened economic, technological and defense ties.

However, analysts say the chances of a major fallout are low as both are committed to countering the rise of a neighboring superpower that they view as a joint concern – China.

“The common wisdom is that the US and India need each other for vital strategic purposes: above all, to mount an effective front in competition with China,” said Daniel S. Markey, senior adviser, South Asia, for the United States Institute of Peace.

“Therefore, they will manage this issue without being sidetracked from that mission. And, to date, the two sides have avoided acrimonious public statements, pledging to take the matter seriously.”

And there is recent past precedent for this kind of pragmatic realpolitik.

The murder in Saudi Arabia’s Istanbul consulate of Jamal Khashoggi, a US resident and Washington Post columnist critical of the Saudi government, caused global outrage and US condemnation at the time. But ultimately the vital relationship between Washington and Riyadh has been stabilized.

In a statement on Monday announcing Wray’s visit, India’s Central Bureau of Investigation – the equivalent to the FBI – said their meeting signified “a step towards deepening cooperation and shared commitment to combat crime in all its manifestations in the spirit of international police cooperation”. — CNN