Just before sunset on Jan. 12, 2016, 10 American sailors strayed into Iranian territorial waters in the Persian Gulf, a navigation error with potentially grave consequences. On their way to a spying mission, the Americans had set sail from Kuwait to Bahrain. It was a long-distance trek that some senior commanders in the Navy’s 5th Fleet had warned they were neither equipped nor trained to execute.

Surrounded by four boats operated by Iran’s Islamic Revolutionary Guard Corps, the U.S. sailors, in two small gunboats, surrendered rather than opening fire. The officer in charge of the mission later said he understood that had a firefight erupted, it could well have provoked a wider conflict and scuttled the controversial nuclear deal the two countries were poised to implement in mere days.

The Navy dialed up an elaborate rescue mission to free the sailors from tiny Farsi Island involving fighter jets and a U.S. aircraft carrier strike group. But the return of the sailors was ultimately secured peacefully. The nuclear deal went forward with the U.S. providing sanctions relief and unfreezing billions in Iranian assets in exchange for Tehran’s promise to curb its nuclear ambitions.

President Donald Trump explicitly invoked the 2016 incident last week as he weighed actions against Iran amid rising tensions. Trump told Time magazine that his predecessor, Barack Obama, had mishandled the high-stakes confrontation, a mistake he would not make. “The only reason the sailors were let go is that we started making massive payments to them the following day,” Trump said. “Otherwise the sailors would still be there.”

But a ProPublica investigation makes clear that Trump’s repeated claims about the captured sailors – Obama’s weakness; that the money was improper – obscure the more troubling realities exposed by the Navy’s 2016 debacle in the Persian Gulf. The Farsi Island mission was a gross failure, involving issues that have plagued the Navy in recent years: inadequate training, poor leadership, and a disinclination to heed the warnings of its men and women about the true extent of its vulnerabilities.

Now, the Navy, and the 5th Fleet based in the Persian Gulf, are staring at the possibility of a military conflict, standing ready for a commander in chief who lacks a permanent secretary of defense and is thus more dependent on uniformed military leaders.

In the wake of the Farsi Island incident, the outlines of the Navy’s fumbles were widely reported. But ProPublica reconstructed the failed mission, and the Navy’s response to it, using hundreds of pages of previously unreported confidential Navy documents, including the accounts of sailors and officers up and down the chain of command. Those documents reveal that the 10 captured sailors were forced out on dangerous missions they were not prepared for. Their commanders repeatedly dismissed worries about deficiencies in manpower and expertise.

Prior to the mission, the sailors had received little training on their weapons, and the crew of one boat forgot to load the limited number of guns at their disposal during the transit. One sailor prepared to record the potentially hostile encounter with the helmet camera she’d been issued but couldn’t get it to work. So she filmed it on her personal iPhone 4. And when they were captured, a rescue seemed unlikely given that no one back at shore had yet realized they were off course.

The Farsi Island episode is consistent with ProPublica’s findings in its ongoing examination of the Navy’s state of combat readiness. ProPublica’s detailed review of the Navy’s two accidents in the Pacific in 2017, which killed 17 sailors from the 7th Fleet, shows that the most senior uniformed and civilian leaders mishandled years of warnings about degraded ships, undertrained and overworked crews, and the potentially fatal costs of tasking vulnerable sailors with an unceasing number of sometimes ill-conceived missions.

Immediately after the release of the Farsi Island sailors in early 2016, Vice Adm. Kevin Donegan launched an investigation that would divide the highest levels of the Navy over the question of who was to blame for the embarrassing incident. The findings of that investigation, completed in February 2016, did not spare the commanders and crew of the two riverine combat boats, or RCBs. They had violated fundamental Navy doctrines regarding navigation and leadership, the report found. Senior 5th Fleet commanders were also faulted and two were relieved of their commands.

Donegan’s investigators, though, dug deeper. They concluded that the riverine unit had not been properly manned or trained before being dispatched to the Persian Gulf. Riverine sailors had had to train themselves. The sailors had done most of their exercises on smaller patrol boats instead of the RCBs used in the Gulf. They had received a minimum amount of training on the latest navigation system. They had never conducted a lengthy training voyage in the open sea, something they would be asked to do routinely in the Gulf.

The investigation’s files included the personal plea of one of the enlisted men taken captive on Farsi Island, Petty Officer 1st Class Kevin Diebold.

“I cannot, nor am I in a position to, determine the exact reasons why my crews were captured,” Diebold wrote. “This is something that should be discussed frankly and openly.”

The seeds of the mishap, Diebold wrote, did not “materialize on the 11th of January, nor do they end, neatly, on the morning of the 13th. It is my hope that the current investigation and the team’s findings are used not to punish 10 sailors, but educate and refocus a critical, if neglected force, if not our Navy as a total warfighting organization.”

The Navy ignored the sailor’s request. In internal Navy memos, commanders criticized parts of the investigation for being “deficient,” “incomplete” and “unsubstantiated” amid disputes over how much training has actually taken place. To address the differing views, the Navy ordered a second investigation and embraced its findings that pre-deployment training and manning for the RCB unit, in fact, had been adequate.

“Pre-deployment training and manning were not contributing factors to this incident,” the second investigation, which was released to the public, concluded.

The Navy’s top commander, John Richardson, signed off on the more reassuring set of findings.

“I’m not prepared to say that there’s a larger problem,” Richardson told reporters in 2016.

Over the weekend, the details of Iran’s downing of an unmanned American drone that further escalated the confrontation remained unclear, but it seemed possible the Navy had again mistakenly entered Iran’s territory. Iran insists the plane had penetrated its airspace; the United States says it was in international territory. Last week, The New York Times quoted an unnamed U.S. official as saying Trump had pulled back in part because of emerging evidence that the Global Hawk drone or a second, manned U.S. spy plane may have indeed breached Iranian territory. Trump cited the high number of possible Iranian casualties.

In a written response to questions, the Navy said it had implemented reforms to improve the coastal riverine units. U.S. trainers now keep careful track of the instruction gunboats and their crews receive while deployed. New maintenance teams are ready to fly into deployed areas to make repairs. The RCB boats have been replaced by a newer gunboat known as the Mark VI.

Rear Adm. Charlie Brown, the Navy’s spokesman, said that many of the changes were still being implemented, but that the Navy’s most senior leaders were confident that “the Coastal Riverine Force is ready to carry out all missions assigned in any numbered fleet area of operations."

Brown also said the Navy’s investigation was “conducted in an independent manner.”

“There were no instances of facts or opinions being silenced,” Brown wrote.

Brown also offered a broader defense of the Navy’s preparedness.

“No naval forces are deployed without ensuring full readiness,” he said. “There should be no doubt — U.S. Navy Forces deployed globally are ready in all respects.”

In an interview with ProPublica on Friday, Donegan, who stepped down as commander of the 5th Fleet in September 2017, said the margin for error is small in such extraordinary circumstances. Training matters. Mistakes can prove dire.

“My biggest concern is about miscalculation,” said Donegan, who now works as a security consultant. “When you have heightened tensions, no direct communications between the two sides and forces in close proximity, an event that one side thinks is low-level might compel the other side to respond in a way that leads to expanded conflict.”

Chapter 1. “What Are We Doing Here?”

To some at the Navy’s outpost in Kuwait, the last-minute mission for which they were briefed on Jan. 11, 2016, seemed preposterous.

The RCBs would have to travel from Kuwait to Bahrain — a 260-mile trip, two times longer than any they’d ever done — carefully avoiding nearby territorial waters. Once there, the National Security Agency, as part of its intelligence operations, would load up their small boats with listening equipment and have them float along the Persian Gulf’s coastline. The mission was given a name: “Radio Creep.” It was unclear who they’d be spying on, but several officers took the order as urgent, and, given worsening weather conditions, one decided the sailors would have to launch within 24 hours.

The crew raised what seemed to be an essential problem: Only one of the three RCBs was currently operational.

They might be able to fix one of the two disabled boats, Gunner’s Mate Isaac Escobedo guessed, but it would be a rush job, he later told investigators.

The boats had been run 3,000 hours beyond the cut off for required overhauls.

Lt. Kenneth Rogers, the officer in charge of the RCB unit, also had concerns. The boats were needed for another mission; to make it to Bahrain, they’d have to refuel at sea, something they’d only done once before — while they were close enough to base to make it home if it didn’t go well; and the crew, if it scrambled to get at least one more boat ready, would be exhausted when it set out, Rogers argued.

Cmdr. Greg Meyer, Rogers’ boss, was sympathetic to Rogers’ concerns, records show, and took the case up the chain of command.

Kyle Moses, the commodore with ultimate authority over the RCB unit, didn’t want to hear any of it. He thought the worried officers were being “overly cautious.” Moses said he didn’t know why so many of his officers were concerned about the riverine command boats making this kind of trip, since “the RCB is a boat and boats float.”

“Navigation is navigation,” Moses, an explosives expert, later told investigators.

The Navy’s 5th Fleet is based in Bahrain and is responsible for about 2.5 million square miles of water and some 20 countries. The vast expanse includes three critical chokepoints at the Strait of Hormuz, the Suez Canal and the Strait of Bab al Mandab at the southern tip of Yemen. The 5th Fleet has been a vital nerve center for American action and interests in Syria, Iraq and Afghanistan.

The 5th Fleet, though, doesn’t have warships of its own and instead relies on vessels and aircraft rotated in from the enormous 7th Fleet in the Pacific as well as stateside fleets.

Riverine boats, if a modest segment of the Navy’s full arsenal of ships and aircraft, have nonetheless been a staple of operations for decades, typically deployed to patrol rivers and marshes, whether they be in Vietnam or Iraq. The RCBs were then the most recent incarnation of the gunboat: 53 feet long, holding crews of eight and loaded with heavy machine guns and high-tech navigation gear.

In the Persian Gulf, the RCBs for years mostly performed escort missions for destroyers and other ships, assignments that kept them in fairly shallow waters for fairly short durations. But in late 2015, the RCBs were pressed into different and more debatable roles. The Navy, overstretched, had just removed a carrier strike group from the region, leaving the Persian Gulf without a U.S. aircraft carrier for the first time in years. The carriers — three football fields long, stocked with dozens of fighter jets and accompanied by other warships — had been a mighty show of force against regional foes like Iran.

Now, to help fill the void, the Navy was going to use three riverine boats. It took barely a month for the 15 sailors in the RCB unit in Kuwait to be confounded — and angry. The idea that their presence served as a show of military might seemed absurd. Sailing flat-bottomed boats designed for rivers in 8-foot waves felt reckless.

Location of Farsi Island in the Persian Gulf

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The unit had just one sailor and one private contractor available for repairs. Getting parts with which to make the repairs was a constant challenge. A delivery of needed parts took 89 days to be shipped. At one point, the sailors were so desperate for basic materials that they bartered Monster energy drinks with the Army unit on base in exchange for paint.

The men spent hours sailing in open waters in the Persian Gulf, launching a reconnaissance drone and filming nothing but empty ocean day after day, week after week.

“What are we doing here?” Escobedo, the gunner’s mate, asked at one meeting with senior leaders. “What is the mission?”

Escobedo’s despair was not isolated. A routine “command climate” survey of Moses’ officers meant to assess morale produced withering results.

“Across the board, the officers hated the command and their jobs,” said Lt. Cmdr. John Pucillo, the director of the Maritime Operations Center.

Moses, the commodore, was incensed by the results, Pucillo told investigators. He summoned all officers to a conference room and went through each complaint individually, demanding answers. The comments were supposed to have been anonymous.

“It felt like it was a witch hunt,” Pucillo said.

On Jan. 11, those who had been pushing back against the mission to Bahrain did what they could to follow orders. Late that night, Escobedo and others stripped parts from one boat to fix a broken water pump to get a second boat ready to sail. The next morning, crews struggled to get the communications gear to work, ultimately succeeding, just before the mission would have been scrapped.

Meyer, the unit’s commander, spoke to the officer who would lead the boats. Lt. David Nartker thought it was futile to argue more.

“My sailors and I can accomplish it,” Nartker told Meyer.

Chapter 2. “I Figured That Someone Would Be Keeping Track of Us.”

At 12:40 p.m. on Jan. 12, Nartker ordered his boats toward the open sea. The repairs had put them hours behind schedule, in danger of being late for the planned refueling with a Coast Guard ship. Nartker decided to take a more direct route to Bahrain than had been planned.

“We were worried about darkness,” Collin Foley, a machinist’s mate fireman, told investigators. “If we can’t find them for whatever reason, we’re out there running on fumes. We’ll run out of gas and be stranded.”

Things didn’t get better.

Nartker had forgotten to order the crew on his boat to load the weapons with ammunition. It was as if the crew had suddenly become blind to the fact that it was traveling in one of the world’s most contested waterways.

Then, the Coast Guard changed the location for the planned refueling. Nartker sought a shortcut. His boat had a computerized mapping program called COGENT as its primary navigation system. He had only received about two hours of formal training on the system back in the United States.

He had one of his men pinpoint the new refueling location on the map. Nartker used the program to draw a straight line to the new spot. The more direct route, he figured, would reach the Coast Guard ship, the USCGC Monomoy, with about 25 minutes to spare before nightfall. Looking at his navigation screen with the view zoomed out to see his entire track rather than a more detailed picture, he saw nothing along the way that was cause for alarm.

Nartker did not tell anyone in his chain of command that he was abandoning his intended course. It was an astonishing lapse of navigational protocol.

“I figured that someone would be keeping track of us,” he told investigators.

The 5th Fleet maintains a series of operations centers to monitor and control Navy activity throughout the Persian Gulf. Smaller stations feed information up the chain of command to larger ones, so that anybody, from a lieutenant in Kuwait to an admiral in 5th Fleet headquarters, has some level of awareness of Navy traffic in the Gulf.

But when it came to tracking the safe transit of the 10 sailors in the riverine boats, that system broke down.

Every 30 minutes, the boats radioed their position to their local operations center in Bahrain. But the sailors there did not plot the coordinates on a map, nor did they always pass them on. The next station up, based in the United Arab Emirates, showed the boats’ course on a computerized map. But the officers using the map had not set it to display the boundaries of sensitive territorial waters around Saudi Arabia and Iran.

One more oversight: During the hectic initial planning, Meyer, the commander of the riverine task force, believed that a Navy ship or plane would be assigned to keep a close eye on the boats in case anything went wrong. His superiors, however, never made such an assignment.

Almost four hours into the trip, several crew members noticed what they told investigators looked like “a bunch of random rocks” off the ship’s bow. Some men thought they were seeing an oil platform.

“I asked what it was,” Foley said. “No one knew. We asked [Nartker]. He had no idea what it was.”

Petty Officer 3rd Class Randall Price, an electronics technician, was passing the time below deck when he got word from other sailors of the unidentified island. He put down the book he packed for the long transit and climbed up to the pilot deck.

Like the other sailors, he couldn’t work the boat’s navigation system for an answer. The screen showed a small purple dot. No name. But Price pulled up a navigational app he’d downloaded on his phone.

He zoomed in on their location. He found the island. He told investigators he saw “a long Arabic name.”

“My curiosity was satisfied,” he said. “I went back down to continue reading.”

At 3:42 p.m., a crew member on the refueling ship, the Monomoy, plotted the boats’ location and realized that Nartker was drastically off course from his original route, the first time that anybody higher in the chain of command noticed the deviation.

The crew member on the Coast Guard ship realized the speck of land about the size of Grand Central Terminal was Farsi Island. It was Iranian territory, and it served as a naval outpost for the Islamic Revolutionary Guard Corps, an elite force of the Iranian military that Trump recently declared a terrorist organization.

The Monomoy immediately called the base in Bahrain on a secure channel to alert it that the boats were headed into Iranian waters.

A sailor in Bahrain noted the Monomoy’s warning in a log. But there is no sign the information was passed any further up the chain of command, or to the sailors on the RCBs.

Chapter 3. “They Got Weapons”

What unfolded over the next 12 hours transformed a bumbling operation into a historic fiasco.

First, one of the boats broke down when the water pump that had worried the crew back in Kuwait fell from the engine block. The sailors decided to stop to make repairs. The gunboats were dead in the water.

“I fucking told everybody this would happen,” Escobedo shouted while he scrambled to repair the damage and his boat bobbed in the waves, powerless.

The sailors then spotted two small boats headed their way. There were only two men on the first boat and just one on the second. They were wearing track suits and sandals. The boats were tiny, roughly 15 feet long.

Then a sailor screamed: “They got weapons!”

The Americans could make out rocket tubes mounted on the pilothouse of one boat. Heavy machine guns were fixed on the bows of both.

Diebold asked for his rifle, which he kept stowed by the boat captain’s seat. There weren’t enough rifles for everyone.

“Each craft was only issued four — I emphasize four — rifles,” Diebold told investigators. “I specifically requested one rifle per crew member, with a minimum of six magazines per sailor. I do not know the reason why I was given less.”

Foley spotted a blue flag atop one of the boats. He pulled out a Navy reference manual. The flag belonged to the Islamic Revolutionary Guard Corps. Foley shouted that the men were Iranians.

Nartker was holding up a wrench and pointing at his engine to indicate to the Iranians that his boat was in need of repair.

Inside the engine room, Escobedo made quick work of the repairs on the water pump and then started up the engines. With each movement, the more maneuverable Iranian boats blocked him and the men aboard them racked their weapons. He could see them squeezing their triggers.

“Stop boat!” they yelled. “Stop boat!”

Nartker decided to ignore the shouting men.

"Go!" he yelled at Escobedo.

Escobedo believed that if he followed the order, the Iranians would begin firing. He thought the rounds would cut clean through their boat. Someone was going to get killed. Rather than gunning the boat, Escobedo simply looked at Nartker: “Sir.”

Nartker later told Navy investigators that he had considered grabbing his M4 assault rifle and trying to shoot his way out. But he thought that if he began shooting he could start a war. He had never received a briefing on the region from the Navy, but he had been reading The Economist magazine. He knew about the looming nuclear accord.

“OK, what's the commander's intent here, the highest commander's intent?” he remembered thinking. “The commander in chief would not want me to start a war over a mistake, over a misunderstanding.”

“English, English, English,” Nartker called to the Iranians. If he could explain through a translator that they were sorry, that they were there by accident, that they were just passing through on the way to Bahrain, maybe the Iranians would just scold them and let them go.

A third boat arrived with five more Iranians with Kalashnikovs. Then a fourth boat with 10 more armed Iranian sailors. None was there to translate.

The Americans felt outmatched. The Iranians ordered the Americans to move away from their guns and take off their body armor. The sailors looked to Nartker. They had been trained to fight. Surrendering felt unnatural. Nartker told his sailors to comply.

Diebold asked one of his men to bring him a photo he kept inside the pilothouse of his wife and son. He was the last sailor to remove his body armor. He was wearing a belt that held his sidearm. It was the last weapon available to the Americans. He pulled off the belt and laid it on the deck.

At 4:32 p.m., the tactical operations center in Bahrain had received the first report from the RCBs about contact with the Iranians. Thirteen minutes later, the boats again reached the operations center by radio with word of the encounter.

The Bahrain center passed word up the chain of command.

“RCBs reporting 2 Iranian vessels are attempting to push RCBs to an unknown island. Iranian vessels had weapons in condition 1 trained on them.”

The battle watch captain in Bahrain couldn't figure out what island the RCBs were talking about. He measured the distance to the nearest island and it was 25 nautical miles to the southwest. But the officer was plotting the position of the boats on the wrong territorial waters map.

The officer did not relay news of the encounter to higher-ups.

The Iranians soon tore down the American flag flying over the lead boat. They raised the blue flag of the Islamic Revolutionary Guard Corps in its place.

The sailors had all been herded onto their lead boat and forced to their knees. Rifles were still trained on them. The Iranians had ripped up one of their own flags into strips to tie the wrists of the Americans.

The weary sailors were soon sitting bootless inside a prayer room on Farsi Island. They leaned on small tufted pillows, staring at their armed captors sitting across from them. A tall Iranian in a maroon sweater vest with coiffed hair and decent English was questioning them. He assumed the small boats, clearly unsuited to the Gulf, couldn’t possibly be alone and must have come from a nearby Navy ship. He directed his questions to Nartker, the only officer.

“Captain David, where is your mothership,” the Iranian asked again and again.

Nartker’s answer that they were simply traveling the 12 hours from Kuwait to Bahrain unescorted was repeatedly dismissed.

“Not possible,” the Iranian said.

The sailors laughed.

“Yeah,” Escobedo said. “I wish you can tell my people that, because we told them these boats can't do that.”

Nartker was taken alone to the Iranian command center to radio a nearby American ship and relay that they had food, water, blankets and access to toilets.

Chapter 4. “Get Our Guys Back”

Vice Adm. Kevin Donegan took a seat in the 5th Fleet combat center. As a young aviator, he had participated in the bombing of Libya in 1986. Later, he spent years directing the fights in Iraq and Afghanistan against Al Qaeda in the Arabian Peninsula. His ascension to command of the 5th Fleet, central to that shadowy battle, was a natural extension of stints at the Pentagon and Central Command.

Minutes after learning of the sailors’ detention, Donegan jumped on a secure line with the head of Central Command, Gen. Lloyd Austin.

Donegan reviewed his plans with Austin and discussed potential options to communicate with Iran. He wanted Iran to know that his intentions were to locate and retrieve the sailors.

More than two hours had passed since the Coast Guard cutter Monomoy had first informed the operations center in Bahrain that Nartker and Diebold were headed for Iranian waters. It had taken an hour and 18 minutes for word to pass up to Kyle Moses that Iranian sailors were pointing loaded weapons at the RCB sailors and attempting to force them to Farsi Island. It had taken an additional 45 minutes for Moses to place the call to Donegan that sent him scrambling toward the battle watch center at about 6 p.m.

Donegan declared a search and rescue operation with the nearby aircraft carrier USS Harry Truman. The designation gave him wide latitude under international law to take actions necessary to rescue the sailors — including entering Iran’s territorial waters. By 6:15 p.m., the USS Anzio, a cruiser, and the Monomoy were sailing toward Farsi Island. Aircraft hurled off the deck of the Truman, located about 40 miles south of the island. F/A-18 fighter jets, an E-2 airborne command center and P-3 surveillance planes raced toward Farsi Island. An Air Force B-1 bomber and F-15 attack jets streaked overhead.

The E-2, which was flying over Farsi Island to coordinate air traffic, made contact with an unknown Iranian official who threatened “tactical action” unless planes left the area. The E-2 pilot did not depart. An official with the Islamic Revolutionary Guard Corps contacted the Anzio, ordering it to “depart territorial waters and proceed to international waters without hostile actions in order to preserve peace and security in the region.” The Anzio kept sailing.

Back in Washington, news of the standoff reached the highest levels of the Obama administration at around noon. John Kerry, the secretary of state, was scheduled to talk about the close-at-hand nuclear deal with Iran’s foreign minister, Javad Zarif, in 45 minutes. Now, the conversation would be completely different.

Kerry told Zarif that the incident was an accident — the result of a mechanical failure. The first priority, he said, was that the sailors be released unharmed as quickly as possible. If that happened, Kerry told Zarif, “We can make this into what will be a good story for both of us.”

Zarif asked that the American military pull back from the island. If that didn’t happen, he told Kerry, it “could trigger a reaction that could be bad for all of us,” according to a senior State Department official with knowledge of the conversation.

Over the next several hours, the men spoke repeatedly. During each call, Zarif expressed increasing confidence that the situation could be quickly resolved. At last, around 3 p.m. Washington time, Zarif promised that the sailors would be released the next morning. It was too dangerous, he told Kerry, to attempt to transfer the men back to U.S. custody in the dark.

On Farsi Island, the Iranians told the sailors, “We’re releasing you.”

One sailor started weeping, and the Iranians swung a camera in his direction to capture his tears for the news.

An Iranian officer then sat down in front of Nartker for one last propaganda coup. He wanted the boat captain to admit they were wrong and apologize on camera. Nartker tried several times to deflect.

In the end, he gave the statement.

Chapter 5. “Set Up for Failure”

Trump had yet to secure the Republican nomination for president at the time of the Farsi Island incident. He quickly jumped on the issue.

“Iran humiliated the United States with the capture of our 10 sailors. Horrible pictures & images. We are weak. I will NOT forget!” he tweeted the day after the incident.

Trump continued to use the incident as a political tool to attack people opposed to his stance on Iran.

Donegan, the commander of the 5th Fleet in 2016, assigned three investigators with nearly two dozen support staff to figure out fault and uncover root causes. They produced a 170-page report based on documents and interviews with every crew member.

Nartker, the report found, had exercised poor judgment in deviating from his initial plan and not properly arming the boat for the possibility of a hostile encounter. Moses, the senior commander, was cited for ignoring warnings, and for having fostered what the report called a “can’t say no” leadership climate. Meyer was faulted for allowing his sailors to develop lackadaisical military practices.

But the report’s findings went beyond the assigning of individual blame. The problems, it found, were more systemic.

At least as far back as 2010, the Navy’s high command had been put on notice about its troubled state of readiness. Retired three-star Adm. Phillip Balisle had issued a scathing assessment: ships were coming apart; the Navy was short thousands of sailors; poorly trained officers were being promoted, making for a generation of unprepared leaders.

Now, Donegan noted similar problems regarding the Navy’s riverine fleet.

“Ineffective pre-deployment training set the stage for the 12 January 2016 incident off Farsi Island,” Donegan wrote in a review that accompanied the report.

After Donegan’s review, the report traveled up the chain of command for several months, receiving commentary at each step.

When it reached Adm. Philip Davidson, responsible for manning and training across the entire Navy, he rejected the findings on manning and pre-deployment training. He instead blamed 5th Fleet commanders for not keeping up standards and training while deployed overseas. Culpability for the Farsi Island episode, Davidson wrote, fell squarely on poor decisions by low-level commanders and the sailors on the captured boats.

A year later, the wider problems of training and manpower in the riverine forces were confirmed in a report by the Government Accountability Office, the investigative arm of Congress.

“We examined the Navy’s effort to address manning, training and equipping problems,” said John Pendleton, who oversees readiness issues for the agency. “The overall readiness of the riverine force was concerning. We made recommendations to address the challenges.”

The Navy insisted on designating some parts of the GAO report secret and other parts sensitive -- meaning its details remained confidential. Congress ordered the Navy to make reforms and report back by January 2018. On Friday, the Navy said it could not determine whether the Secretary of the Navy had delivered such a report.

But Pendelton said the Navy has not yet fixed all the problems identified.

“The Navy has yet to address many of the persistent problems, especially manning,” Pendleton said.

Davidson, Moses and Meyer either did not respond to requests to comment or declined to comment for this article.

Some Navy officials wondered if Davidson’s conclusion was a missed opportunity to look at the bigger picture.

In 2017, the year following the Farsi Island incident, there were four major collisions in the western Pacific. The worst involved the USS Fitzgerald and the USS McCain, which each collided with cargo ships, leaving 17 sailors dead.

Davidson, still in charge of manning and training, was tapped to help assess the significance of the collisions. He found that manning shortages and poor training factored in both. Admirals, officers and sailors were held to account.

Davidson, though, was soon promoted and now holds one of the most coveted positions in the American military as head of the Indo-Pacific Command, in charge of all military branches in the region.

In recent months, the Navy has come under fire over whether it has made good on its promises to fix its readiness problems, criticism that has taken on new urgency given the escalation of tensions in the Persian Gulf.

During testimony several months ago, Davidson told Congress the reforms had all been completed, only to be publicly corrected by other Navy officials, who admitted they had not been. Challenged by the Senate Armed Services Committee to account for the pace of reform, Davidson provoked derision by noting that the vast majority of the Navy’s ships had not crashed in the summer of 2017.

“I want real numbers. I don’t want general ‘We’re working on staffing’ or ‘We’re working on more training,’” Sen. Angus King, I-Maine, told Davidson.

The Navy brought charges against several sailors involved in the Farsi Island surrender, including four officers and two enlisted men. The Navy dropped charges against one officer. The rest of the men took guilty pleas that resulted in no jail time but ended their chances of career advancement.

With punishments resolved, the Navy recommended kicking four officers out of the service. But the four panels of officers charged with reviewing the cases, known as boards of inquiry, ruled that the men’s conduct was not severe enough to merit expulsion.

Rogers, the aviation officer in charge of the Kuwait naval outpost, received a favorable ruling allowing him to stay in the service.

“I reported significant problems to my chain of command and I was ignored,” Rogers wrote in his appeal.

Nartker also appeared before a Navy panel to make his case for remaining in the service. The panelists, all superior officers, found some fault with his conduct. But they also concluded that he should remain in the Navy.

The officer in charge of the panel, Capt. Steven Fuselier, was especially opposed to the Navy’s decision to pursue Nartker’s ouster. In an unusual move, he asked for a dismissal of all findings against the young lieutenant.

Nartker’s superior officers had ignored protests. They had assigned him a mission beyond the capabilities of the gunboats. And they ordered him to proceed, even knowing about the shoddy equipment and the late start.

It was wrong to punish him, when so many others shared responsibility. Nartker, Fuselier wrote, “was set up for failure.”