The first man to die was the ship's cook who had just prepared a meal for the crew and was standing on the bridge of the Sage Sagittarius as it cruised 840km off the Far North Queensland coast.

Cesar Llanto, 42, was taking his last voyage from his home in the Philippines on the Japanese-owned, Panama-flagged coal carrier.

He had told his wife Nelia that once he returned, he would buy a second-hand car and invest the rest of his earnings in their children's future.

But at 8am on August 30, 2012, the Sage Sagittarius was passing through the Coral Sea, cruising south, when Cesar Llanto vanished.

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Within hours, Australian authorities had ordered the ship to turn around and a full-scale land-and-sea search for the missing cook began.

Back in Japan, in the offices of the ship's Japanese operator, Nippon Yusen Kaisha Line, superintendent Kosaku Monji, 37, launched an investigation.

Ship of death crew member Jessie Martinez (above) claimed a culture of bullying aboard the Sage Sagittarius which he had threatened to expose. Photo / Supplied
Ship of death crew member Jessie Martinez (above) claimed a culture of bullying aboard the Sage Sagittarius which he had threatened to expose. Photo / Supplied

After 30 hours the search for Cesar Llanto was called off. He was never seen again.

Under orders from Nippon Yusen, Kosaku Monji was dispatched to Brisbane where he landed on the Sage Sagittarius via helicopter.

Reportedly he found a terrified crew, some of whom had barricaded themselves into their cabins.

The ship was then diverted to Port Kembla, near Wollongong, where the Australian Federal Police boarded the vessel and began interviewing crew members.

Among them was the ship's chief engineer, Hector Collado, but none of the crew offered much explanation.

Later, it would be reported that Mr Collado had called his wife Rebecca back in the Philippines with a warning that there had been a threat on his life.

Allegedly, he asked that when he returned home multiple cars be used to pick him up from the airport, and that no one was to know which car would take him from the port to his house.

Two weeks after Cesar Llantio's disappearance, the Sage Sagittarius was preparing to enter the port of Newcastle.

Harbour pilots landed on board as the bulky 70,000 tonne carrier was set to pick up its next load of coal.

It was 8am on September 14, around the same time that Mr Llanto had vanished, when Hector Collado plunged to his death.

The fatal fall took the 57-year-old 12m down an engineering shaft from one deck to the next. He was found with a "curved wound" on his head.

Crewmen aboard the Sage Sagittarius as it enters Newcastle Harbour. Photo / News Corp Australia
Crewmen aboard the Sage Sagittarius as it enters Newcastle Harbour. Photo / News Corp Australia

Superintendent Kosaku Monji had remained on board the ship, conducting an internal audit for the NYK line, as it sailed for Japan.

It was the morning of October 3, 2012 when the Sage Sagittarius docked back in Japan.

Kosaku Monji remained on board to supervise the unloading of the coal.

The following morning, at 7.27am, the crew made the discovery of Monji's body.

He had been entangled and then crushed by the ship's large unloading rollers.

Since the three deaths, a series of investigations have indicated a bullying culture on board, threats against a gay inmate and allegations of gun smuggling.

An inquest opens on Thursday at the Coroners Court in Sydney into the deaths of Cesar Llanto and Hector Collado. Kosaku Monji's death in Japan is outside the NSW Coroners' jurisdiction.

The court has previously heard that the deaths of the chief cook and chief engineer on the ship bound for Australia were highly likely to have been a result of foul play.

Allegations had been made against the ship's captain, Venancio Salas, of physically assaulting crew and pressuring them to buy guns from his contacts.

Tensions between the captain and one of Cesar Llanto's staff had allegedly intensified in the days before the cook's disappearance.

Jessie Martinez, 26, who worked in the mess for Llanto, had been pressured into admitting he was gay, and had been punched and verbally abused on board.

With Llanto as his defender, Martinez had written an explosive letter threatening to delay the ship, loaded with its consignment of coal in Newcastle.

Following Llanto's disappearance, Mr Collado became "deeply distressed" in the weeks before his own death.

A forensic pathologist told an earlier Coroners Court hearing that Mr Collado's death was suspicious because his head wound appeared unrelated to the injuries from the fall.

The inquest at the NSW Coroner's Court in Glebe is expected to be concluded on Thursday, with findings delivered at a later date.