It has been dubbed the ship of death. In 2012 three seafarers met their fate while working aboard the Sage Sagittarius, a giant transport ship which ferries coal between Australia and Japan.

Four Corners has pieced together the events on board using the accounts of crew members themselves.

On August 30, 2012 the MV Sage Sagittarius was weeks into a routine voyage to Newcastle.

Alone in the Coral Sea, about 470 nautical miles from the Queensland coast, the ship was on course to pick up its next load of coal from Newcastle Port on schedule.

As dawn broke, the 42-year-old chief cook, Cesar Llanto, woke and began his daily rounds in the galley, mixing mincemeat for that day's meal.

It had been an unusually tense few weeks.

Llanto's subordinate, 26-year-old messman Jessie Martinez, was part way through his first contract at sea.

Martinez's initiation had been rougher than most.

Martinez was bullied into declaring he was gay; which only made the bullying worse. His crew mates scoffed at his discomfort; one observed he was "always crying".

Thousands of miles from home, Martinez was alone with his tormenters. The only figure with the power to stamp out the behaviour on board was the ships' captain, Venancio Salas.

But Salas was himself one of the chief culprits.

The captain took a dim view of Martinez, and was irritated by the missteps and stumbles of the first-time sailor.

"He tried to chat back when I try to tell him something," Salas later explained to the Australian Federal Police.

"He always had ... reasons ... There has been so many, many lapses, and errors and everything and I've been trying to correct him."

In fact, Salas assaulted the cook's hand whenever the whim took him.

It took Martinez several days to recover from one punch Salas had landed in his kidney one morning in the galley - the messman had not greeted his captain suitably.

Salas demanded Martinez write him a grovelling letter of apology, then rejected several first attempts as insufficiently remorseful.

"Things have been so difficult for me from the moment I started," Martinez wrote.

"I really had a hard time to figure out the best way to do my responsibilities ... Things didn't work out the way I wanted it to be."

Letter reveals homophobic harassment, gun smuggling onboard

Sorry, this video has expired Video of Sage Sagittarius crew members shown at inquest

Martinez saw the cook Llanto as an older brother, and his only potential protector.

Llanto told him he would speak with the captain on Martinez's behalf.

But as the ship neared Australia in August 2012, Martinez instead considered writing a complaint to the Australian Maritime Safety Authority and the International Transport Workers' Federation.

He was being urged on by the 35-year-old oiler, Raul Vercede.

Sitting together Vercede and Martinez drafted the complaint listing Martinez's concerns: "Overtime not paid", "harassment", "humiliation", "threatening contract termination".

And as a final note, "gun smuggler".

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Salas had been peddling semi-automatic side arms to his crew — 9-millimetre and .45 calibre weapons that he sold for more than $600.

He flashed handgun catalogues to his staff when they came to the bridge or the engine room, and it was clear he expected his crew to make a purchase.

He got a clip on each transaction.

Martinez's complaint letter was explosive.

It threatened not just to delay the ship in Newcastle, but even the livelihood of the captain whose primary responsibility was the swift return to Japan with a ship full of coal.

A late shipment was also not a good reflection on the rest of the crew whose jobs depended on arriving on time.

Cook goes missing, body never found

Sorry, this video has expired 'Not easy' for a seafarer to fall overboard, say MUA officials

The skies were overcast on the morning of August 30. A rough wind was blowing across the bow of the ship as it ploughed the water at a steady 13 knots. The seas were heavy, but aboard the hulking 70,000-tonne vessel the waves were barely noticeable.

The ship would come within communication range of the mainland that day, and, under the guidance of his superior, chief cook Llanto, Martinez was rethinking his plan to send his complaint.

The sun had barely breached the horizon when he decided not to send the letter, and to instead confess his plan to the captain.

Llanto, furious and angry, rushed after him, his hands still oily from the mince he had been preparing that morning.

On the bridge Martinez found not the captain, but the chief officer.

As the words spilled out of his mouth — about the complaint, about Vercede and the plan to blow the whistle the cook, Llanto barged in, but it was too late.

He barely spat out a sentence when he was cut off by the chief officer, his superior.

Martinez was marched to the doorway of the captain's cabin and ordered to destroy the complaint.

With the crisis averted, the captain settled in for his breakfast, but soon noticed something odd — the cook was not in the galley for breakfast.

After a search of the ship failed to locate Llanto, concern turned to alarm.

Soon search parties were organised aboard.

Within two hours Australian authorities were contacted and a full-scale land-and-sea search began for the missing cook.

The ship turned around.

As every hour passed, the odds of the cook having survived in open water plummeted. After 36 hours, the search was called off.

Half a world away, in the headquarters of the ship owner in Japan, a telephone rang.

It was picked up by the man responsible for the Sage Sagittarius, superintendent Kosaku Monji.

A former ship's engineer, the Sage Sagittarius was one of three ships he had under his control. That day, reports rolled in of the cook lost at sea.

Investigation hampered by mismatched alibis

In short perfunctory emails he ordered the captain to collect statements from the crew, directing them to detail their whereabouts during the crucial moments before the cook disappeared.

As these statements spilled out of his fax machine in Japan, Monji studiously marked up each sailor's whereabouts on a spread sheet.

Most crew members had alibis, but a handful did not.

One discrepancy was blindingly obvious; two men claimed to be in the galley at the crucial time but both swear that they were there alone.

The only witness was frustratingly vague on the matter. He was also one of the most senior officers on the ship, the chief engineer, Hector Collado.

Under orders from his superiors, Monji was dispatched to the ship to calm the crew.

Within days he arrived in Brisbane where he landed on the ship via helicopter, accompanied by two Caloundra security guards.

He found a terrified crew.

Some had barricaded themselves in rooms. Others only dared to walk the ship in twos or threes.

Adding to the tension, the ship had now been contacted by the Australian Federal Police, who had diverted the ship to Port Kembla.

On September 7 the ship was met by an army of AFP officers as they berthed at Port Kembla.

News cameras captured the arrival of the ship as it lumbered into port.

Forensic officers completed an exhaustive search taking finger prints, DNA swabs, seizing telephone records, log books and engine read-outs.

They also searched the ship's incinerator but found nothing but ash. It had been seven days since the death, and any forensic evidence of value had now been contaminated.

During police interviews, a fearful crew offered little. Detectives examined the key witness, engineer Collado.

During an unrecorded interview they spoke with him, but he said almost nothing and they felt certain he was holding something back.

The oiler Vercede and messman Martinez left the ship along with three other crew members, but tensions remained.

The ship left Port Kembla for Newcastle where the AFP planned to interview the remaining crew. During the short voyage, some began to notice the engineer Collado acting strangely.

Rumours circulated that he wanted to change his statement to police.

Alone in his cabin he packed his bag and prepared for his disembarkation at Newcastle; he would fly home after leaving the ship.

He called his wife in the Philippines, telling her that he feared he was being followed.

He instructed her to take an unmarked car to the airport and to leave the grandchildren at home.

Chief engineer met grim end as ship sailed into Newcastle

On September 14 the ship neared Newcastle. Harbour pilots landed on deck via helicopter as tug boats pulled alongside the ship to steer it into berth.

Deep inside the ship, the engine room hummed. It was a cavernous space filled with valves, boilers, stairwells and elevators. Collado walked the upper levels more than 11 metres from the engine-room floor.

Down below, the engineers sat awaiting orders. The engine room was alive with noise but even above the din the engineers started at the sound of a loud bang. Surely a burst valve. Some ventured out to inspect. What they found shocked them. Lying, face down, was the mangled body of chief engineer Collado.

Waiting at Newcastle, AFP officers were told the frustrating news. They were now forced to delay their interviews while the NSW Police conducted their own.

This time forensic officers flooded the ship moments after the death.

They soon made a grim discovery; a trail of blood near the railing where the chief engineer fell.

An autopsy report later confirmed their suspicions; something or someone had struck the chief engineer before he plummeted to his death. It was now a homicide investigation.

The deaths became front-page news in Newcastle. On September 15, one by one, crew members walked into Waratah Police Station, a short drive from the port, to be interviewed by NSW Police.

They were terrified, and police gleaned little from their interviews.

Within days their investigation suffered another setback when the captain and all the crew except one, boarded planes and flew back home.

Both the AFP and NSW Police were in an impossible predicament, left to investigate two suspected homicides with no witnesses and no suspects to interview.

Third death aboard the Sage Sagittarius

On the evening of September 18, four days after Collado's death, the Sage Sagittarius steamed out of Newcastle.

But one man still had a chance of getting to the bottom of the deaths. The company man, superintendent Kosaku Monji, who was left on the ship. On board he began an internal audit on behalf of the ship's operator, NYK Line.

Now laden with coal, over two weeks the ship retraced its path back to Japan from Australia, arriving in Japan's busy Kudamatsu Port on the morning of October 3, 2012.

Almost immediately, the ship began unloading its cargo using vast on-board conveyer belts, powered by giant mechanical rollers.

It took three days to unload the ship. Monji remained on board to supervise. On his last night he sat down with the new captain to discuss his internal audit.

It was an early start the next day and he returned to his cabin at 9:00pm, but was still up and sending emails up until midnight.

Unloading began before daybreak the following morning. Coal streamed off the ship via the rapid conveyer belts into containers below.

Around 3.15am a strange sound was heard coming from the rollers powering the conveyer belts and Monji, torch in hand, investigated.

Hours passed. Unloading continued. Around 7:27am a crew member made a grisly discovery — a human leg protruding from the rollers. The conveyer was stopped and Monji's body was removed. He was dead.

His body was finally brought ashore around 9:30am.

Japanese coast guard determines death was 'self fault'

Two days later, the AFP learned of Monji's death back in Australia.

On October 30, three weeks later, AFP officers contacted the Japanese police via Interpol and asked about the circumstances surrounding the fatality.

Crucially, they asked whether "Japanese authorities believe there are any links between Mr Monji's death and the two other incidents".

Two months later they received a one-page response: "As for the death of Mr Monji, the Japan Coast Guard determined it as self fault."

Japanese police passed the investigation on to the Japanese Transport Safety Board, which handed down its report almost 12 months later.

The board were never told about the deaths of the chief cook or the chief engineer.

Its report found that it was "probable" the death was an accident, but that "it was not possible to determine the situation in which [Monji] was trapped ... because there were no witnesses of the accident".

'I am putting my whole faith in the AFP', says Cook's widow

More than two-and-a-half years later the wife of chief cook Llanto sat in front of a video camera in a board room in the Philippines.

Nelia Llanto was weeping and struggling to speak among great, heaving breaths.

Her image was being beamed more than 6,000 kilometres away into a court room in Sydney, where a handful of lawyers were hanging on her every word.

"I am putting my whole faith in the AFP," she said.

The AFP officer who led the investigation watched her testimony from the front row inside the court room, sitting alongside his NSW counterpart along with a throng of journalists, lawyers and union representatives.

It was now the NSW Coroner's turn at trying to get to the bottom of the deaths and Nelia Llanto was testifying via video link.

Despite the years, the grief was still raw and she begged the court for justice.

"Have pity on my children. I put my faith in you," she said.

Watch Four Corners: Ship of Death tonight at 8.30pm on ABC. The program will also be available on ABC iView.