Some were unconscious as they were taken from the fishing vessels, others collapsed against each other. One man who did not regain consciousness was treated by a Medecins Sans Frontieres [MSF] team and taken to hospital in an Italian navy helicopter. A refugee is carried up the gangway of the Swedish Coast Guard ship as it rescues 441 people; 52 people died in the hull. Credit:Kate Geraghty As they collapsed on the deck of the MY Phoenix, many simply put their heads on their knees, closed their eyes and slept. Others stared out at the great expanse of sea they had just crossed, faces etched with the grief of all they had left behind. In the hull of one wooden boat, 52 people lay dead, overcome by diesel fumes during their 12-hour journey. Their bodies were recovered as fellow passengers looked on, the boat that took them to their death was sunk once darkness fell. Soon after 1pm, another boat appeared in the water, this one a rubber dinghy carrying at least 100 refugees, also attempting to make the journey from Libya to Italy.

The operation suddenly took on new urgency – there were now nearly 1300 refugees in danger of drowning. Refugees on a wooden boat carrying 565 people are rescued off the Libyan coast by Migrant Offshore Aid Station crew. Credit:Kate Geraghty Along with a large Swedish Coast Guard ship and the Phoenix, an Italian warship arrived in the area to take part in the rescue. By the end of Wednesday, more than 3000 people attempting to make this crossing had been rescued, according to the Italian Coast Guard. Some of the 441 refugees attempting to cross from Libya to Europe on a wooden boat are rescued by the Swedish Coast Guard off Libya. Credit:Kate Geraghty

As night fell and the sea turned an inky black, 150 men were still to be taken from the second wooden boat, dehydrated, seasick and dreading another night in the stinking, unseaworthy vessel. Fairfax Media boarded the stricken vessel and spoke to some of the refugees on board. Refugees continue to flood into Europe. Pictured: a woman aboard a European ship after being rescued in the Mediterranean. Credit:Kate Geraghty "I lived a good life for four years in Libya," Wassim, 30, of Pakistan, says, leaning against the broken wooden railing of the vessel that carried him just 30 nautical miles off the coast of Libya. "Now Daesh [Islamic State] is arresting all the Africans, putting them in jail and forcing them to fight … soon they will come to arrest the Pakistanis and the Bangladeshis. They have already taken some of us."

A refugee sits in despair on a wooden fishing boat as he waits to be rescued off the coast of Libya. Credit:Kate Geraghty As he watched the sun dip lower over the horizon, his friend and countryman, 28-year-old Azzam, described the deteriorating security situation in the Libyan town of Sirt, where he worked in the aluminium business. "There is not a minute where there is not fighting; nowhere is safe for us," he says. An unconscious refugee is evacuated from the MY Phoenix by MSF and Migrant Offshore Aid Station crew to an Italian warship. Credit:Kate Geraghty Their journey began at 2.30am on Wednesday, as people smugglers drove them in vans with blackened windows towards the Libyan coastline.

When they arrived at the edge of the Mediterranean they were forced to wade into the water and then swim out to the fishing boat, where they were hoisted aboard. Mohamed, 25, of Pakistan, in the hull of the wooden fishing boat that he shared with the 52 people who died. Credit:Kate Geraghty More than 150 people were forced to travel in the hull, trapped in a fog of diesel fumes, becoming sicker and sicker as the boat rocked in the swell for more than 12 hours. They had paid 1800 Libyan dinars ($1870) for the journey. "It is a miracle no one died here," Azzam says, staring at the broken boards and cracked hull as water splashed around the engine room and the boat groaned against the strain. Back on board the MY Phoenix – a search and rescue ship run by the Migrant Offshore Aid Station with the support of MSF – more than 415 refugees sat on two decks, the frenzy of the rescue operation replaced by quiet exhaustion.

Syrians, Libyans, Pakistanis, Bangladeshis and Iraqis are squeezed onto the overcrowded decks with Moroccans, Filipinos, Sudanese, Nigerians, Ghanaians, Palestinians, Tunisians, Eritreans and Ethiopians. There is little room to lie down to sleep – the ship is already over capacity – but at least for now they are safe. There is water, food and medical attention and soon the MY Phoenix will be under way, powering towards a port in Italy where these people, who have fled the ferocity of war, brutal dictatorships and human rights abuses, will take another step towards their uncertain future. Ruth Pollard and Kate Geraghty are aboard the MY Phoenix at the invitation of Medecins Sans Frontieres.