In the frenzied weeks following the assassination of President John F. Kennedy, on November 22, 1963, the C.I.A.’s counter-intelligence staff was thrown into the eye of the raging investigative storm. And Pete Bagley, a former fieldman who’d spent a derring-do career in the back alleys of Europe, was suddenly sent back into the field: a long-dormant K.G.B. asset had come alive.

The intel that the Russian, Yuri Nosenko, delivered over drinks in the Geneva safe house left Bagley astonished. Nosenko had been personally involved in the K.G.B.’s investigations of Lee Harvey Oswald, both before and after the Kennedy assassination.

Within days, Nosenko, accompanied by a burly C.I.A. bodyguard, was flown to America. Yet during subsequent interrogations, Bagley decided the Russian was reciting a carefully written script. Nosenko’s real purpose was, as they say in the trade, “source protection.” He’d been dispatched to protect a high-ranking mole already embedded in the agency.

When Nosenko returned from a lulling vacation in Hawaii (the trip, including the services of a red-haired prostitute, paid for by U.S. taxpayers), harsher interrogations began. For two years, the Russian was interred in a 12-by-12-foot windowless concrete room.

Yet Nosenko never broke. Instead, a no-holds-barred feud erupted inside the agency between the Russian’s accusers and his champions. And Bagley was one of its victims. First, he was branded “paranoid.” Next, a year-long investigation probed whether he, in fact, was the mole. Bagley was cleared and sent off to Brussels as station chief, but when his tour ended, he retired. “The tide,” he’d realized, “had already turned against me.”

But then a death—purportedly a suicide—wrenched Bagley from his retirement, pulling him back to the shadowy battlefields of his former life. He embarked on his final mission, his last chance to get to the bottom of the betrayals that had scarred not just the agency but also his own professional life.

A Death in the Agency

It was just after nine, a fresh Monday morning, September 25, 1978, when Robert McKay, an ancient mariner who made his living crabbing the waters of the Chesapeake Bay, looked up from the weather-beaten deck of his boat and saw the sloop coming straight at him. Its big white sheets spread by the crisp autumn wind, the sailboat must’ve been doing seven knots, hell-bent, and on a collision course.

Yet somehow the sloop managed to fly by without making contact. And as it passed, McKay saw that there was no one at the Brillig’s tiller. He watched as the sailboat headed swiftly toward shore, until, as if spent by its exertions, it came to a weary halt, trapped in the mud off Hays Beach. Then he radioed for help.

Maryland park ranger Gerald Sword was the first to board the grounded sloop. When he climbed on deck, he found no sign of anyone, just unspent 9-mm. cartridges scattered about.

Warily, he descended below. The galley table had been broken, and papers littered the floor. As best he could make out, they were government reports. Stray words caught his eye: “missiles,” “Soviet Bloc,” “satellite.” And at the top of many of the pages was a stamped advisory that riveted his attention like a warning beacon: CLASSIFIED, TOP SECRET.

Continuing his search, Sword noticed an open leather briefcase. He extracted a letter. It was addressed to John A. Paisley, apparently a Washington Post employee involved with subscriptions. The writer was angry, complaining that the deliveries of the Post had been erratic, but payment was enclosed for what had been received. A guy who delivers newspapers owns a fancy sailboat like this?, the ranger wondered incredulously.

It was only as Sword was about to leave the cabin that he realized the ship-to-shore radio had been operating, emitting small, weak squeaks the entire time. Twisting the dial to Off, he saw the carefully arranged row of electronic consoles spread across a lower shelf. He decided these were something out of the ordinary, not your everyday ship-to-shore transmitting equipment. Yet why have this kind of sophisticated gear on a sailboat? Perplexed, he hightailed it to his jeep to radio his report.

Once the Brillig was towed to the Coast Guard station, the Maryland State Police were notified and the search for the boat’s owner began. A call was placed to The Washington Post, where John Paisley apparently worked. Only there was no one with that name employed at the paper, and the ID number on the letter found on the boat belonged to another employee. What was going on?

The state police soon had its answer, or at least the beginnings of one. Two officers from the C.I.A.’s Office of Security came and took charge of the boat. When the Coast Guard and state police protested, the two C.I.A. men offered a terse explanation: national-security issues took precedence. Over the next two days, teams of agency officers carted off boxes of papers and electronic equipment from the boat.

When Maryann Paisley, who’d been separated from her husband since August, was at last informed of what was still officially a missing-person’s case, she immediately went to John’s bachelor apartment in downtown Washington. It had been ransacked. Probably the work of the agency’s Office of Security, she decided. And it seemed to her that they’d been looking for something specific.

But she didn’t complain about the breaking and entering. And she didn’t run to the press to share the news that her husband, the spy, was missing. She, too, knew firsthand how business was conducted in the clandestine corridors of power.

Then, a week later, a body was found.

A call was placed to The Washington Post, where John Paisley apparently worked. Only there was no one with that name employed at the paper.

Despite two sets of diver’s belts—38 pounds of weight—wrapped around the corpse like the tight bands encircling a sarcophagus, it’d floated to the surface of the Chesapeake Bay. Decomposition and the greedy nibbling of local crabs had rendered the body beyond recognition.

The autopsy recorded that the deceased was a five-foot-seven-inch, 144-pound white male. A single gunshot behind the left ear was the cause of death; it had fractured the skull as devastatingly as if a grenade had exploded inside the cranium.

Establishing the identity of the deceased proved more problematic. The corpse’s blood type could not be resolved, since there was insufficient blood remaining in the body. Fingerprinting was also a challenge, since the skin on the hands had decomposed. And a dental identification would be difficult, since only partial upper and lower plates remained intact after a week in the bay.

Yet Baltimore’s chief medical examiner did not hesitate to sign a report declaring that the deceased was John Paisley. The papers were dated October 1, 1978, the day before the Medical Examiner’s Office received the body. The official cause of death: suicide.

Several days later, the body was picked up by a suburban Virginia funeral home that had a cozy relationship with the C.I.A. Maryann Paisley, who somehow had never gotten around to viewing the corpse, signed an order for its cremation. Later, though, she’d assert that she’d never signed anything.

With the remains reduced to ashes, it seemed likely that any further interest in the suicide on the Chesapeake Bay would go up in smoke, too. The institutional process of forgetting could begin.

The papers were dated October 1, 1978, the day before the Medical Examiner’s Office received the body. The official cause of death: suicide.

But about a month later, in November 1978, a small Wilmington, Delaware–based newspaper got hold of “the strange death of a spy,” revealing for the first time that the alleged suicide in Chesapeake Bay involved a high-ranking C.I.A. employee. Soon the national press jumped into the fray.

Despite all its years of practice, the C.I.A. remained such poor liars. A bemused C.I.A. spokesman publicly dismissed John Paisley as a “low level analyst,” adding that when Paisley had retired years earlier, he’d lost any access to secret documents.

In swift order, journalists shredded the official disclaimers. It was established that in the course of a distinguished 20-year career, Paisley had risen to the upper echelons of the agency. And while he’d ostensibly retired two years before, Paisley was still involved in hush-hush work. He continued to have operational access to the agency’s most closely guarded intelligence secrets—its sources and methods for knowing the latest Soviet nuclear developments.

Then it was definitively revealed that the sloop had been outfitted with a top-secret burst transmitter, and that this was a device largely used by spy agencies for covert communications with satellites. However, whether the transmitter was used to communicate with our birds or the Russians’ remained the stuff of heated speculation.

And was the body really Paisley? While the medical examiner had been certain, the corpse had been unrecognizable. As for fingerprints, the C.I.A. spokesman claimed that although it was standard practice to store employee fingerprint records, Paisley’s had, incredibly, been “inadvertently destroyed.”

More disconcerting discoveries followed: Paisley’s Merchant Marine file listed him at five feet 11 inches and weighing 170 pounds. Plus, while the remnants of the underwear on the recovered body had a clearly marked 32-inch waist, the BVDs filling a drawer in Paisley’s apartment were size 36.

In fact, when scrutinized, the official verdict of suicide seemed to fall apart. The gunshot wound was above the left ear. Would Paisley, who was right-handed, have chosen to reach awkwardly across his body to deliver the fatal shot? And what of the diving weights? Was that Paisley’s attempt to cause his body to sink without a trace? If so, why? And what about the facts that there was no blood, brain tissue, or, for that dumbfounding matter, a gun or even an expended cartridge aboard the Brillig?

The Maryland State Police cleverly swept away those annoying details. Paisley, according to the scenario they shared, had crisscrossed his body with 38 pounds of lead weights, then trundled to the side of the boat and, with one colossal effort, leaped overboard—but not without first managing to reach across his chest and, while in midair, shoot himself above the left ear. It would have been, some wags suggested, an acrobatic maneuver nearly as nimble as the police investigators’ explanation.

Meanwhile, in Brussels, the retired spy Pete Bagley read about the strange death of John Paisley. And it started him thinking. He had worked with Paisley, and he now wondered if it had been Paisley’s body that had been hauled from the bay. Had Paisley actually taken his own life? Or was the mystery of this suicide another piece in the long-running puzzle Pete had been trying to put together for years?

Prodded by the macabre image of a corpse wrapped in chains, Pete decided the time had come, he’d write, to “bring old mysteries out of the dark.” He would “set out on my own” to find “the mole who had never been discovered.” He booked a ticket to Washington. He didn’t use an alias; he hadn’t thought to cache a passport with a work name. Yet he should have known there was no such thing as a retired spy.

Howard Blum is the author of several books, including Night of the Assassins. His latest book, The Spy Who Knew Too Much: An Ex–CIA Officer’s Quest Through a Legacy of Betrayal, will be published on June 7