ALBANY — Theirs was a relationship built on nearly three decades of unswerving loyalty, absolute trust and near-constant interaction: It was all but impossible to imagine Gov. Andrew M. Cuomo without Joseph Percoco, his closest aide and the enduring mainstay of his life in politics.

It took only a few days to send it crumbling to the ground.

By the end of April, it had become clear that Mr. Percoco was in trouble. Federal investigators had subpoenaed records related to him from a state ethics board. Then, the governor learned that federal agents had raided Mr. Percoco’s home in Westchester County, looking for evidence that he and his wife had improperly received thousands of dollars from companies that had done business with the state.

Later, after some 72 hours of intense strategizing, the governor effectively cut ties with Mr. Percoco in a jarring public statement acknowledging that the actions of “some individuals” may have “defrauded the state.” Mr. Cuomo has been even more overt since then, repeatedly naming Mr. Percoco and another former aide, Todd R. Howe, as the prime targets of the investigation led by Preet Bharara, the United States attorney for the Southern District of New York.

As Mr. Cuomo, a Democrat, rose from politician’s son to Washington prodigy to attorney general and governor, his life and career have been grounded by Mr. Percoco, whose role as Mr. Cuomo’s all-purpose troubleshooter, alter ego and Capitol ambassador involved him in virtually all that the governor’s office touched, from its multibillion-dollar upstate economic revitalization efforts to its short-lived anticorruption commission — both of which have drawn the attention of federal investigators.

The scope of Mr. Bharara’s investigation remains hazy. What does seem clear, however, is that Mr. Percoco’s success in the administration belied growing financial struggles and other pressures going back to a personal bankruptcy filing in 1995. Friends and associates often heard him and his wife imply that his government salary never stretched far enough.

And after it became known that Mr. Percoco was to leave his post as executive deputy secretary to take a job as a senior vice president at Madison Square Garden, the governor explained then that he had been influenced by familial and financial concerns.

Mr. Percoco has not been charged with any crime, and he did not respond to requests for comment. His lawyer, Barry A. Bohrer, has called his client “a dedicated and effective public servant” who was proud of his work for “the people of the state of New York.”

But for both the governor and the man who had always taken care to do his bidding — no more, no less — their split was an emotional Waterloo.

For Mr. Percoco, being cut off from the Cuomos is probably particularly painful: He started working for Mr. Cuomo’s father, former Gov. Mario M. Cuomo, as a 19-year-old. The suggestion that he may have gone astray has rattled Cuomo’s circle, especially the governor, who is said to have been blindsided by the news of his aide’s investigation.

“If it turns out that his closest adviser was gaming the system for his personal enrichment, it strikes at the heart of how the governor describes his own administration,” said Blair Horner, the executive director of the New York Public Interest Research Group, a government watchdog. Mr. Horner added that although the direction of the investigation remained unclear, “If it plays out badly for Percoco, it plays out badly for the governor.”

For Mr. Cuomo, 58, who has been steeped in politics since he was a teenager, the political is the personal. That made Mr. Percoco, 47, part of the family and, therefore, profoundly powerful.

In his 2014 memoir, published just before Mr. Percoco’s return to the administration after a stint running the governor’s successful re-election campaign, Mr. Cuomo praised him as “the total package: trained as a lawyer, he had the guts, brains, and stick-to-itiveness necessary to attack any project — hard.” During the “worst of times,” Mr. Cuomo recalled, “he could make us laugh.”

Interviews with two dozen former colleagues, political associates and Albany veterans depict Mr. Percoco as the consummate logistics and operations ace, guided by the same get-things-done-now ethos as Mr. Cuomo. He was the verbal assassin, tearing down relationships one day and asking favors the next; the governor’s combination lieutenant and fishing buddy, to whom Mr. Cuomo could turn for a soothing dose of guy talk — and, when the job required, for political warfare.

As an enforcer and organizer, he was indisputably effective: helping to whip a slim majority out of a Republican-led Senate to pass statewide marriage equality in 2011; working to coordinate the state’s response to Hurricanes Irene and Sandy; and choreographing Mr. Cuomo’s events and, by extension, his public persona.

“He was a no-nonsense type of gentleman,” James P. Molinaro, the former Staten Island borough president, said. “He said something to you, and it stuck.”

With a bodyguard’s build and a bouncer’s demeanor, Mr. Percoco has been making things stick for the Cuomos for more than two decades.

Stories of his menacing punch are everywhere in Albany, where Mr. Percoco dealt with labor and lobbyists, environmental advocates and business leaders, teachers’ unions and charter-school activists alike.

A frequent opponent was the administration of Mayor Bill de Blasio, the governor’s principal sparring partner in politics.

Shortly after the mayor — whose open feud with the governor has dominated New York politics in recent years — won funding for New York City’s prekindergarten classes in 2014, Mr. Percoco ran into a mayoral aide at an event.

Expecting a hello, the aide received a warning instead, according to a person who was present and requested anonymity because of the investigation of Mr. Percoco.

“You got us this time, but we’re coming for you,” Mr. Percoco said, according to the person. “We’re going to destroy you.”

‘My Father’s Third Son’

In a sign of his once-central place in the Cuomo family firmament, Mr. Cuomo once referred to him as “my father’s third son, who I sometimes think he loved the most.”

Their closeness sprang, in part, from natural affinities, despite an age gap of more than 10 years. Both knew their way around a car engine. Both were Italian and had daughters, not sons. Both liked to fish. Mr. Cuomo may have been the son of a governor, comfortable in the public spotlight, but Mr. Percoco’s middle-class roots in Rockland County resonated with what Mr. Cuomo saw as his own bootstrapping Queens past; the governor loved to talk about driving a tow truck to help put himself through law school.

The men eventually came to live within about 15 miles of each other. In 2012, the Percocos moved from their modest Staten Island home to a roomy blue house in the well-groomed Westchester enclave of South Salem, using a two-year, $800,000 balloon mortgage from a company led by Abraham Eisner, a prominent liaison for the state’s Orthodox Jewish community for the governor. The house cost the Percocos $815,000, only a little more than the amount of the mortgage.

The move put them in the same lush, horse-farm-studded landscape as Mr. Cuomo and his girlfriend, the television hostess Sandra Lee, who live in Mount Kisco.

With his old-school, almost military bearing, Mr. Percoco had a profound respect for hierarchy. Though he might privately criticize Mr. Cuomo, he would brook no criticism of “the gov” or “the governor,” as he called him, from others.

Yet for all Mr. Percoco’s unquestioning loyalty, Mr. Cuomo — known as a demanding boss — did not hesitate to criticize him, calling out his shortcomings, professional and otherwise.

Mr. Percoco seemed to take the jabs in stride. At a birthday party for Mario Cuomo in 2012, Mr. Percoco joked about Andrew Cuomo’s frequent digs at his weight and his sartorial choices.

“Andrew’s the older brother that I never had,” he said, “and never wanted.”

He stuck by Mr. Cuomo in the bitterest period of his career, after his humiliating withdrawal from the 2002 governor’s race and subsequent divorce from Kerry Kennedy. It was Mr. Percoco who set up the announcement where Mr. Cuomo dropped out of contention; it was Mr. Percoco who went with Mr. Cuomo on a therapeutic fishing trip to Long Island Sound a few days later; and it was Mr. Percoco who served as Mr. Cuomo’s “divorce counselor,” as the governor later wrote in his memoir. “Joe” was among the first people Mr. Cuomo turned to for advice on mounting the comeback that brought him to the attorney general’s office in 2007.

“I think you are crazy for wanting to go through it again,” Mr. Percoco said when Mr. Cuomo floated the idea of running during another fishing trip to the Hamptons, according to the memoir. “But I’m game if that’s what you want to do.”

Once Mr. Cuomo was elected governor in 2010, Mr. Percoco rarely touched on the intricacies of policy. But his passion for perfecting every last detail of events — and for burnishing Mr. Cuomo’s image — was well-known on the Capitol’s second floor, where he occupied an office near the governor’s.

If the governor did not recognize someone, Mr. Percoco, standing at his shoulder, supplied the name. If an announcement on Long Island needed staging, he made sure the banner looked good, the right people were there (and the wrong people were not), and the room was cool enough to prevent a sweat. If a negative quote appeared in the press, he would be on the phone, irreverent humor shifting to a lacerating bark when he sensed a lack of cooperation.

At an event in Ithaca during Mr. Cuomo’s 2010 campaign for governor, an anti-fracking protester handed one of Mr. Cuomo’s daughters a CD with information about the controversial drilling technique.

It was not long before Walter Hang, an anti-fracking advocate, received a phone call, Mr. Hang recalled. Mr. Percoco was on the line.

“They saw this as an affront,” recalled Mr. Hang, who had been expecting to meet with Mr. Cuomo that afternoon. “He barks at me, ‘They’re your people.’”

The meeting was permanently off.

Some appreciated his direct style, which made Mr. Percoco the most feared man in state government — perfect, in other words, for the job.

“It seems everyone in politics and government likes candor and honesty until you tell them something they don’t want to hear,” Robert Zimmerman, a Democratic strategist who knows Mr. Percoco, said. “Joe was upfront with political figures and New York State officials. That enabled him to be an effective negotiator.”

The Investigation

In April 2014, he left the administration — where he was earning $155,974 a year — to run Mr. Cuomo’s re-election campaign, earning $225,725 in salary and expenses, including a $120,000 bonus. Sometime that year, Mr. Percoco also began consulting for COR Development and CHA Consulting, companies with business before the state, later reporting in a financial-disclosure filing that they had paid him between $70,000 and $125,000. Both have been subpoenaed in the federal investigation. (COR has denied paying Mr. Percoco.)

That same year, Mr. Percoco’s wife, Lisa Toscano Percoco, a schoolteacher from Staten Island and his college sweetheart, was paid between $75,000 and $100,000 by a Democratic Party operative in Connecticut with ties to Competitive Power Ventures, a Massachusetts-based company seeking to build a power plant in the Hudson Valley of New York, subject to state approvals.

The timing of the couple’s earnings — and Mr. Percoco’s employment by the state — is believed to be a focus of the investigation.

While he was running the campaign, he still periodically played the role of bodyguard. During a Labor Day parade in 2014, Mr. Cuomo was repeatedly approached by Zephyr Teachout, his liberal challenger in the Democratic primary for governor. Without so much as a word from the governor, Mr. Percoco physically blocked Ms. Teachout.

Mr. Percoco may have thought he was done with the Cuomo administration after the election, but he returned in late 2014 with a substantial raise and to a looming personal crisis for the governor. Indeed, Mr. Percoco was often at Mr. Cuomo’s side as Mario Cuomo was dying at the end of 2014, according to the governor’s schedule, later helping to arrange funeral services and acting as the guest-list gatekeeper. At the funeral, as Mr. Cuomo consoled his mother, Matilda, Mr. Percoco could be seen standing just nearby.

By the time Mr. Cuomo’s second term began last year, he was a rare member of Mr. Cuomo’s original inner circle remaining in the administration. The governor’s counsel, his chief of staff, and his director of state operations had all departed for the private sector, making Mr. Percoco more crucial than ever.

That October, the two men flew to Kansas City, Mo., for the Mets’ appearance in Game 1 of the World Series. Mr. Percoco finally left the administration for good on Jan. 4.

Less than four months later, federal investigators served a subpoena on Mr. Cuomo’s office in Albany, seeking a range of information about its dealings, including the Buffalo Billion, the governor’s signature economic initiative.

By this spring, the inquiry had appeared to focus on Mr. Percoco.

Now Mr. Percoco, the problem-solver, could hobble both the administration and the legacy of the man who was everything to him.

“Has it been a deeply troubling situation for myself? Certainly,” Mr. Cuomo said on May 2, less than a week after the federal raid. “I know Joe Percoco for many years, and he is a good man, and I would be shocked if he did anything wrong. But let’s get the facts, and then we can all make our own decisions.”