Preet Bharara, the United States attorney when the criminal complaint was unsealed, said at the time that there were “no allegations of any wrongdoing or misconduct by the governor anywhere in this complaint.”
But Mr. Percoco and Mr. Cuomo were close political and personal allies for more than two decades, and Mr. Percoco’s presence in a federal courthouse has the potential to reflect badly on both Mr. Cuomo’s choice of friends and his choice of personnel.
The allegations against Mr. Percoco involve graft at the highest levels of the executive branch of state government.
“There is a lot for the public to be concerned about here,” said Susan Lerner, executive director of Common Cause New York. “This trial raises pay-to-play questions. This trial raises issues of using public resources for private gain.”
“It raises significant issues about how discretionary funds used for economic development are handled in our state, billions — literally billions — of taxpayer dollars.”
Mr. Percoco was indicted along with Alain E. Kaloyeros, the former president of the State University of New York Polytechnic Institute, and six executives of companies that had done business with the state; the defendants have all pleaded not guilty. Prosecutors had charged two overlapping bribery and fraud schemes, in a case that grew out of a federal investigation into the Cuomo administration’s upstate economic revitalization plan, known as the Buffalo Billion.
Mr. Percoco is to be tried with three of his co-defendants; a second trial, which will include Mr. Kaloyeros as a defendant, will be held in June.
“We think that a fair and open-minded finder of fact will conclude that Mr. Percoco is not guilty,” his lawyer, Barry A. Bohrer, said last week. “We look forward to the trial.” Michael C. Miller, a lawyer for Mr. Kaloyeros, had no comment.
In the trial, the prosecution’s star witness is expected to be Todd R. Howe, who pleaded guilty in 2016 to charges associated with the bribery scheme and has his own longstanding Cuomo connections.
A onetime aide to Mario Cuomo, Mr. Howe had been friends with Mr. Percoco since Mr. Howe hired him out of college to work as an advance man for Mario Cuomo. Mr. Howe later worked for Andrew Cuomo when he was the secretary of Housing and Urban Development in Washington and, in 2014, he and Mr. Percoco shared an office during Andrew Cuomo’s 2014 re-election campaign for governor, in which Mr. Percoco was the campaign manager.
Prosecutors said in a criminal complaint that in order to disguise the nature and source of the bribes that companies paid to Mr. Percoco, they funneled the payments in some cases through bank accounts and a shell company set up by Mr. Howe, who they had retained to help them obtain official state favors.
“This case is about a scheme that was cooked up between Todd Howe and Joe Percoco to line Joe Percoco’s pockets with money from clients of Howe, who had business before the state,” a prosecutor, Janis Echenberg, told Judge Valerie E. Caproni in December.
To conceal their schemes in their emails, Mr. Percoco and Mr. Howe used the code word “ziti” — a term used in “The Sopranos” — to refer to bribe payments, the complaint said.
Prosecutors have alleged that the energy company, Competitive Power Ventures, which was building a power plant in the Hudson Valley, paid more than $287,000 in bribes to Mr. Percoco, which were funneled through a “low-show” job for his wife, Lisa Toscano-Percoco, in return for official actions that benefited the firm. (She has not been charged.)
The prosecutors also accused COR Development, a Syracuse-area developer, of paying about $35,000 in bribes to Mr. Percoco for his help in, among other things, reversing a decision by the state’s economic development agency.
As the governor’s go-to “enforcer” for political agendas, Mr. Percoco was responsible for tactics — persuasion in some cases, outright threats in others — that have engendered bad blood among many of Mr. Cuomo’s political opponents and even his friends. And few of those seemingly slighted by Mr. Percoco — and by extension, Mr. Cuomo — are likely to be running to the governor’s defense in the event that the trial generates negative headlines.
The Percoco case marked the second time that Mr. Cuomo’s administration had been investigated by the Southern District prosecutor’s office; in January 2016, Mr. Bharara announced the end of “a thorough investigation” into the governor’s interference with an anticorruption panel that he had created and then abruptly shut down, saying there was “insufficient evidence to prove a federal crime.”
“Cuomo’s political opponents could try to use this case to damage the governor, no matter the outcome,” said Hank Sheinkopf, a Democratic political strategist who has worked both for and against the governor in campaigns.
“He has done well to separate himself from the other Albany scandals,” Mr. Sheinkopf added, “and now a scandal created by someone close to him is going to trial.”
In his 2014 memoir, “All Things Possible,” the governor described Mr. Percoco as “the total package: trained as a lawyer, he had the guts, brains and stick-to-itiveness necessary to attack any project — hard.” And Mr. Cuomo added that “during the worst of times,” Mr. Percoco could also “make us laugh.”
Mr. Cuomo said when the charges were announced that if they were true, he would be “saddened and profoundly disappointed.”
“I have zero tolerance for abuse of the public trust from anyone,” the governor said. “If anything, a friend should be held to an even higher standard.”