At some point on Wednesday, a Danish cargo vessel, carrying tons of the world’s deadliest chemical weapons, will sail into an Italian port and carefully begin transferring its lethal cargo onto an aging American merchant ship.

The U.S. MV Cape Ray, specially outfitted with two massive machines to neutralize those weapons, will then head out to sea, where it will turn mustard gas and nerve agents into polluted water. By September, the Cape Ray will deliver the remains of Syria’s chemical arsenal, the third largest in the world, to ports in Texas and Finland for disposal as industrial waste.

Since it began last fall, the international effort to find, verify, pack, transport and ultimately destroy the Syrian weapons has been unprecedented in countless ways.

Never before have such lethal substances been packaged in bullet-proof containers and carried on flatbed trucks through the front lines of a war zone. Never before have such weapons been destroyed at sea.

There have been setbacks, delays and arguments. On at least one occasion, as some of the loaded containers sat for months on a ship in the hot Mediterranean sun, toxic vapors leaked.

The effort has involved sustained cooperation by dozens of countries, some of them sworn adversaries.

The U.S. MV Cape Ray will neutralize some of Syria’s deadly chemical weapons. (Department of Defense)

Completion of the job means little, if anything, to the millions of Syrian civilians still suffering in a cauldron of civil war. It is unlikely to stop a single barrel bomb dropped by government military forces on their fellow citizens, or the breathtaking cruelty of Islamist militant fighters in Syria or neighboring Iraq.

Still, officials involved in the effort say, it has diminished the prospect of additional pain and suffering, and has reduced the world’s stockpiles of lethal chemical weapons. By such measures, it was a success.

“I’m relieved we have been able to come as far as we have with this operation, always knowing this is only the beginning,” said Sigrid Kaag, who heads the joint mission of the United Nations and the Organization for the Prohibition of Chemical Weapons (OPCW) in Damascus, which oversaw the effort. “It’s not the end, looking at the Middle East, looking at the country, and what’s happening to the people.”

A destruction device

As the war in Syria expanded during the summer of 2012, the government of President Bashar al-Assad acknowledged for the first time that it possessed chemical weapons. It would never use them against Syrian citizens, a Foreign Ministry spokesman said, but they could be deployed in the face of “external aggression.”

Within the Obama administration, which was under pressure to aid the rebel forces trying to overthrow Assad, the primary concern was that the arsenal might “get into the wrong hands,” a senior administration official said, suggesting the weapons might be stolen or taken over in a violent assault on the storage and production facilities dispersed across Syria.

According to accounts provided by several administration and other Western officials, some of whom spoke on the condition of anonymity about the past two years of Syria policy, those fears were compounded by the growing power of Islamist extremist forces, with ties to al-Qaeda, within the Syrian opposition.

By the end of the year, the United States had launched discussions among a group of Western allies to examine scenarios of chemical weapons breakout and how to manage them.

In Washington, the Pentagon was tasked with developing options and capabilities to secure the arsenal. “The initial thinking was that we might have to go into Syria and destroy the [chemical] sites,” the senior administration official said, an option that would require thousands of troops, by some calculations, and a “transportable” destruction machine they could take with them.

As planning continued, the Pentagon’s Defense Threat Reduction Agency began working on such a device. By June 2013, the first field-deployable hydrolysis system had been built and tested. The size of a large transport container, it was a low-tech mechanism that required only a few chemicals to partially neutralize the weapons material and a lot of water to dilute them to the toxicity of industrial waste.

But during the third week in August, reports that Syria had used the weapons in the eastern suburbs of Damascus changed the U.S. calculations.

Obama quickly threatened to punish Assad with air attacks against his weapons-delivery systems. Asked at a Sept. 9 news conference in London whether there was “anything at this point that [Assad’s] government could do or offer that would stop an attack,” Secretary of State John F. Kerry replied with frustration and dismissal.

“Sure. He could turn over every single bit of his chemical weapons to the international community in the next week. Turn it over, all of it, without delay, and allow a full and total accounting for that,” Kerry said. “But he isn’t about to do it, and it can’t be done, obviously.”

Within hours, as the secretary was flying home over the Atlantic, Russian Foreign Minister Sergei Lavrov was on the phone. Perhaps, he said, Assad really could turn over the weapons to international control.

Before the end of the day, the Syrian government had publicly expressed interest. U.S. officials speculated that Assad was being pushed by the Russians, feared an American attack, or was simply buying time to continue the war. Whatever the reason, Liz Sherwood-Randall, the senior White House aide in charge of the weapons crisis, said in retrospect, “this was an opportunity to be seized.”

Over the next few weeks, Kerry and Lavrov had developed a plan for the international community to take control of the weapons and destroy them; the United Nations had approved it; an international OPCW team was on the ground in Damascus; and Syria had submitted a formal declaration of its chemical weapons materials that closely corresponded to U.S. and other intelligence assessments.

The end of June 2014 was set as a deadline for the complete destruction of all chemicals, equipment and facilities. The question, the senior official said, was how.

Making it up as they went

Headquartered in The Hague, the OPCW is charged with implementing the international Chemical Weapons Convention, to which 190 countries belong and which Syria was now prepared to join. It monitors compliance and verifies destruction, although it had never attempted anything like the Syrian operation.

Kaag, the high-ranking Dutch U.N. official named to head the mission, had long experience in the Middle East but none in nonproliferation or weapons of mass destruction. She and officials from the United States, Russia and other nations, working together, made it up as they went along.

“The whole process was evolutionary . . . pragmatic” and cooperative, Kaag said.

Syria’s weapons facilities were to be destroyed on the ground by the Syrians under OPCW supervision, a process that included using “cutting torches and angle grinders to destroy or disable a range of items . . . [that] included missile warheads, aerial bombs and mixing and filling equipment,” an OPCW news release said.

The question was what to do with the chemicals themselves. In the past, chemical weapons destruction had always been a static undertaking, with materials burned in place. There was agreement that such an undertaking was impossible in the midst of the Syrian war and that the material would have to be removed.

Several countries said they would send ships to the Syrian port of Latakia to retrieve the arsenal, with the bulk transported by Norway and Denmark, which agreed to take the most dangerous, “Priority 1” material. Initially, the idea was to take the chemicals to another country to destroy them. But of more than a dozen governments approached, none agreed.

“Countries were getting shy. They were worried about environmental impact and risk,” Kaag said. “It was understandable.”

The solution was to take the two portable machines that had been manufactured the previous year, weld them to the deck of the Cape Ray, and destroy the chemicals at sea. It had never been done before.

Help from Iran and Russia

The Syrians were charged with packing the materials in specially made containers, but international officials who were supposed to supervise them often could not get to the war-torn sites. “It was too unsafe for us to be there,” Kaag said. “We had to trust the Syrians.”

They were given GPS trackers and cameras that could transmit live pictures to U.N. and OPCW officials. “We would equip them, walk them through the protocol” and then watch them as they packed material that in most cases had been seen and labeled by inspectors on previous visits, she said. After their training, the Syrians were presented with international certificates making them official handlers of hazardous materials.

Before chemicals could be moved, they often had to be transferred from barrels that had sat in place for decades. Routes had to be planned and safety precautions put in place, including training health officials and sending materials to hospitals and clinics along the highways in case of attack or other mishaps that sent toxic gas spewing into the atmosphere.

When a shipment arrived in Latakia, the port was closed for 48 hours while the containers were loaded onto the ships. When leaks were detected in containers aboard one of the ships, the vessel returned to Latakia so the chemicals could be repacked. There were no injuries.

Although Syrian government officials sometimes balked, they were largely cooperative, in contrast with their unwillingness to help other U.N. agencies in the delivery of humanitarian goods to besieged populations, Kaag said.

At times, the process bogged down because of combat in areas where chemical facilities were located or because of a lack of needed supplies. Much of Kaag’s time was occupied negotiating with the Syrians or soliciting other governments — including Iran, Assad’s other backer — to apply pressure or help in other ways.

The Iranians, she said, provided technical advice. “They obviously lived through a terrible chemical weapons experience themselves,” when the Iraqi forces of Saddam Hussein made liberal use of chemicals during the 1980s Iran-Iraq war. “They see themselves as quite committed to eliminating the use of chemical weapons anywhere.

“They’ve also been helpful to us in contacts with Syrian authorities . . . in amplifying our messages, validating our approach,” Kaag said.

Russia, despite growing conflict with the United States over Ukraine and overall Syria policy, continued to cooperate on the chemical weapons project, said a second Obama administration official. U.S. diplomats formed a triumvirate with their U.N. and Russian counterparts and communicated regularly to address problems as they arose.

‘What next?’

As the June 30 deadline approached, the removal hit a snag, with 8 percent of Syrian chemicals remaining at a site about 70 miles from Damascus. There was fighting with militants of the Islamic State of Iraq and Syria along the road to Latakia, the Syrians said, and it was too dangerous to travel.

U.S. and other officials, using their own surveillance resources, confirmed the problem but continued to press for completion. “It put a stop to all operations for weeks,” Kaag said. “We’re not military security analysts,” but the approach in such situations, she said, was always to say: “ ‘We hear you, but you need to resolve this. What are you planning? What do you expect? What can we tell [U.N.] member states’ ” who have set the deadline?

“This particular site was one of the most dangerous,” she said. “You think, ‘What next?’ You keep talking to the Syrians — ‘What are your plans?’ . . . The security argument was wearing thin, and patience was wearing out.”

Alternative plans, including landing aircraft and flying out the remaining chemicals, were considered and rejected as too risky.

With only 10 days left before the deadline, the trucks finally began to move. On June 23, the OPCW announced that the remaining chemicals had arrived in Latakia and were loaded aboard the Danish vessel, the Ark Futura.

The OPCW mission will continue in Syria, making sure that all remnants of the chemical program are gone.

But having finished what they set out to do, Kaag and Sherwood-Randall, the White House aide, agreed to share a glass of champagne the next time they met.

The lesson she drew, Sherwood-Randall said, was that “we have to be inventive, entrepreneurial, collaborative, seize the initiative, and be relentless about getting it done. This is one we can be proud of.”