A military judge found Seaman Recruit Ryan Mays not guilty on Friday of setting fire to a $1.2 billion Navy ship.

Mays, 21, had stood trial on charges of aggravated arson and willfully hazarding a vessel for the four-day blaze that destroyed the USS Bonhomme Richard, an amphibious assault ship, in 2020.

The acquittal marks the end of a two-year ordeal for Mays, who spent 55 days in the brig after he was arrested.

“I can’t get everything I’ve lost back, but today is the start of my new life,” Mays told ProPublica in a statement. “I am grateful that the military judge saw me for who I am: an innocent man who wanted to serve his country. This fire was traumatic for me and a lot of other sailors. This court-martial is an added layer of trauma.”

On July 12, 2020, the Bonhomme Richard was moored at a San Diego Navy base and undergoing a major overhaul. That morning, an area of the ship known as the “lower V” caught fire, and the blaze quickly spread throughout the vessel. The warship was lost and had to be decommissioned.

A ProPublica investigation into Mays’ case found there was little to connect him to the fire. There was no physical evidence that Mays — or anyone — purposefully set the fire. The Navy had one witness who placed Mays at the scene shortly before the fire but whose story changed over time.

The criminal investigation into Mays also stood at odds with another Navy inquiry into the fire, which found that 34 people, including five admirals, either directly led to the loss of the ship or contributed to it. That investigation uncovered a litany of failures that put the ship at risk for a catastrophic fire, including poor training, insufficient oversight and dangerous storage of hazardous materials. Additionally, 87% of the ship’s fire stations were out of order.

The Navy continued to pursue Mays even after a military judge recommended this year that the case be dropped for lack of evidence after a probable cause hearing.

In closing remarks, Mays’ lead defense attorney, Lt. Cmdr. Jordi Torres, said the investigation was a “live-fire exercise in the dangers of confirmation bias.” He said investigators and then the prosecution discounted any evidence that didn’t fit the narrative of Mays as the arsonist.

The lead prosecutor in the case, Capt. Jason Jones, told the judge, “You’re allowed to use inferences and circumstantial evidence” in making a determination of arson. Jones said criminal cases are like puzzles, and even when there is a missing piece, the picture is still clear.

Jones also addressed some of the findings of the other Navy investigation in his closing remarks, saying the prosecution didn’t dispute that the ship was lost to firefighting failures. But, he said, the fire started as a “sucker punch from behind” that the Navy couldn’t have prevented.

In the nine-day court-martial, the Navy had alleged that Mays was a disgruntled sailor who had gone down to the lower V with a bucket of flammable liquid, set the fire and then snuck out a hatch, changed his clothes and slipped back among the sailors on duty.

Mays was 19 at the time of the fire, assigned to menial jobs such as mopping and painting. He had previously dropped out of SEAL training and had told fellow sailors that the special warfare program was where he thought he belonged. Being on a ship he disliked, the prosecution said, was his motive.

Investigators found a blue Bic lighter in Mays’ possessions and have pointed to it as the possible way the fire was started. Torres was dismissive, saying “apparently just having a lighter makes you an arsonist.”

The trial largely centered on two competing witnesses and arguments over whether a crime had even been committed.

Fire investigators with the Bureau of Alcohol, Tobacco, Firearms and Explosives ruled the blaze an arson that was started by someone putting an open flame on large cardboard boxes. But defense experts disputed that conclusion, saying that there were two other possible causes ATF investigators missed and that “undetermined” was the only reasonable conclusion. The defense experts testified that lithium batteries and arcing from an engine wire on a forklift could not be ruled out as causes of the fire.

Phil Fouts, the fire investigator who testified on behalf of the defense, said he could not with any scientific certainty say whether the batteries, the forklift or arson was more likely the cause of the fire.

An ATF electrical engineer testified that he did not take any pictures or notes about the batteries during his examination of the scene, even though the batteries were found in the area that the agency identified as the origin of the fire. The batteries were then stored in a Home Depot bucket by ATF investigators. The engineer also did not photograph the forklift. The engineer testified that upon further inspection and testing of both the batteries and the wire, he did not think either caused the fire.

Trying to rebut the defense experts’ findings, the ATF engineer showed the judge a presentation using a forklift photo to highlight why he thought it couldn’t have caused the fire — but the photo was of the wrong forklift. There were two in the lower V, and the defense expert had found evidence of arcing in the other forklift.

Jones said that arson cases are often based on circumstantial evidence and the government had done its due diligence in reexamining the possible causes brought up by the defense.

The prosecution’s key witness, Petty Officer 2nd Class Kenji Velasco, testified that while he was standing watch the morning of the fire, he saw Mays go into the lower V shortly before he spotted smoke. Velasco at first told Naval Criminal Investigative Service agents he couldn’t identify the person he saw, but over several interviews he changed his story to say he was sure it was Mays. Velasco said the person he saw was wearing coveralls, but several witnesses testified they saw Mays in a different uniform that morning.

In an unusual twist, the prosecution did not call the lead NCIS agent to the stand. However, defense lawyers did call agent Maya Kamat to testify. The defense mainly questioned Kamat about an alternative suspect she investigated for several months. Another witness told NCIS she had spotted the sailor, Seaman Recruit Elijah McGovern, sprinting from the lower V around the time she saw smoke that morning.

Miya Polion, who is now out of the Navy, testified she saw McGovern jump over a cone that had been blocking off the lower V. “It’s kinda weird to be running on the ship,” she said, so she kept looking at him the entire time he was in view.

The prosecution claimed that video evidence showed Polion could not have seen McGovern that day because there was too much contractor equipment, such as scaffolding and dumpsters, in the way.

When interviewed by NCIS agents, McGovern denied setting the fire. McGovern had been searching online for fire characteristics the morning of the blaze and had a drawing on his phone depicting steps to set a coffee shop on fire. McGovern had told agents that the searches were research for a book he was writing about dragons, and that the novel began with a ship on fire.

Kamat testified she stopped investigating McGovern because he left the Navy and NCIS no longer had jurisdiction. Several months later, the Navy charged Mays with the crimes.

In response to prodding by the prosecutor during cross-examination, Kamat agreed that she also stopped investigating McGovern because she had exhausted all leads.

In closing arguments, Jones dismissed McGovern as a sci-fi loving sailor who had been seen leaving the ship and had been properly cleared as suspect.

The Navy and Capt. Derek Butler, the military judge, have refused to release nearly all records in Mays’ case, citing Article 140a of the Uniform Code of Military Justice as well as a memo issued by the former Defense Department general counsel and Navy interpretations of that guidance. ProPublica has filed a complaint and motion for a temporary restraining order and preliminary injunction to prevent the Navy from continuing to withhold court records in Mays’ case, contending that the Navy and the judge are violating the First Amendment and common law rights of access to court proceedings and records.

During the court-martial, exhibits also weren’t always visible, including photographs of key evidence, and stipulations of fact, sometimes to correct testimony, weren’t publicly available.

“There was never any evidence to support a conviction, and that’s about the only thing that makes sense about this court-martial, because Seaman Mays is innocent,” Torres told ProPublica on behalf of the defense team. “Thankfully, the military judge based his verdict on the evidence and not on mere argument and supposition. The Navy won today because an innocent sailor avoided a wrongful conviction.”