The scheme described by federal prosecutors could upset a key element of President Biden’s foreign policy agenda: bolstering ties with India.

Federal prosecutors on Wednesday charged an Indian national in a murder-for-hire scheme targeting a Sikh separatist and activist in New York who is a U.S. citizen and has been outspoken in calling for a Sikh-majority homeland.

The assassination plot was organized by an Indian government official and linked to the June killing of a Sikh separatist in Canada who was fatally shot by masked gunmen outside a Sikh temple, according to an indictment filed in federal court in New York.

Together, the charges announced in New York and the earlier slaying threaten to complicate relations among the United States, Canada and India and could hurt President Biden’s efforts to cultivate Indian leaders in a bid to counter the global influence of China and Russia.

Here are five takeaways from the foiled plot, as described by prosecutors.

The New York plot was focused on a prominent Sikh separatist.

The indictment identifies the person who was targeted to be killed in the conspiracy only as the “victim,” but American officials said he was Gurpatwant Singh Pannun, the general counsel for the New York-based group Sikhs for Justice. Mr. Pannun is a vocal proponent of independence for Punjab, a northern Indian state that is home to a large number of Sikhs.

Sikhs constitute a powerful minority group in India, and the goal for separatists like Mr. Pannun is the creation of a sovereign Sikh state known as Khalistan. Mr. Pannun and Sikhs for Justice have been banned from India because of their activism.

An Indian government official with “intelligence” experience drove the plot.

The Indian official is not named in the indictment but is said to have been “employed by the Indian government as a ‘senior field officer’ with responsibilities in ‘security management’ and ‘intelligence.’” The official also made reference to having served in India’s Central Reserve Police Force and to having been trained in “battle craft” and “weapons.”

The man charged in the plot had described trafficking drugs and weapons.

Nikhil Gupta, the Indian national, is charged with murder for hire and conspiracy to commit murder for hire. He was recruited by the Indian official in May, the indictment says. An apparent selling point for his landing the job was his telling the Indian official that he had experience as an international trafficker of drugs and weapons.

At the Indian official’s direction, the indictment says, Mr. Gupta contacted a person he thought was a criminal associate for help hiring a killer. That person turned out to be a confidential source for the U.S. law enforcement authorities and introduced Mr. Gupta to a purported “hit man” who was actually an undercover law enforcement officer.

In dealings arranged by Mr. Gupta, the Indian official agreed to pay the undercover officer $100,000 to carry out the killing, the indictment says.

The New York plot had connections to a Sikh activist’s killing in Canada.

On June 18, masked gunmen killed Hardeep Singh Nijjar, a Sikh activist and an associate of Mr. Pannun’s, outside a Sikh temple near Vancouver. Hours later, the indictment says, the Indian official sent Mr. Gupta a video clip that showed Mr. Nijjar’s bloody body slumped in his car. About an hour after that, the official sent Mr. Gupta the New York target’s street address.

The next day, according to the indictment, Mr. Gupta told the person he understood to be the hired killer that Mr. Nijjar “was also the target” and that “we have so many targets.” Given Mr. Nijjar’s killing, Mr. Gupta added, there was “no need to wait” to kill the New York target.

The day after that, the indictment says, the Indian official sent Mr. Gupta a news article and a message about the New York target that said “it” was a “priority now.” Mr. Gupta was arrested in the Czech Republic on June 20 at the request of the U.S. authorities.

The New York plot and the killing in Canada may have major geopolitical implications.

Despite growing concerns about India’s commitment to democracy, bolstering ties between Washington and New Delhi has been a key element of Mr. Biden’s foreign policy agenda as he seeks a counterbalance to the power of Russia and China.

Justin Trudeau, Canada’s prime minister, has already accused the Indian government of involvement in Mr. Nijjar’s killing. U.S. officials, having gotten wind of the plot to kill Mr. Pannun, expressed concerns to Indian leaders about the planned assassination days before the charges against Mr. Gupta were announced.