If US and Russia strike a deal in Geneva, inspectors may soon be embarking on a task that has never been tried.

The job of an international chemical weapons inspector is one of the most dangerous in the world. Inspectors have to seek out some of the most poisonous substances known to mankind and dismantle bombs filled with deadly nerve gas. So it is remarkable that, after more than two decades of chemical weapons destruction, not a single inspector has been killed.

But Syria presents a new kind of challenge. For if the US and Russia strike a deal at Geneva and the government of president Bashar al-Assad does not rescind its application to join the chemical weapons convention (CWC), the inspectors could soon be embarking on a task that has never been attempted: disarming a country of its weapons of mass destruction in the midst of a war.

In the few days inspectors were on the ground in Damascus looking for evidence of the 21 August poison gas attack, they came under sniper fire that put one of their vehicles out of action and confined them to their hotel for a day.

The task of tracking down, verifying and then destroying perhaps more than 1,000 tons of mustard gas and nerve agents scattered over scores of military sites will be complex, time-consuming and risky. But the half dozen current and former inspectors interviewed by the Guardian all argued it is worth trying.

"Just getting Syria to join the chemical weapons convention is an enormously important and historic step forward," said Paul Walker, the program director at Green Cross International advocacy group and a veteran of the two-decade effort to destroy US and Russian chemical weapons. "Once you have the sites highly secured, inspected and locked down under seal that is another big step forward. Then if the weapons are used again there would be huge consequences."

Jean Pascal Zanders, who runs The Trench, a research and consultancy initiative focusing on disarmament, said: "We really are in uncharted territory here, and there is going to be a need for creativity … but if countries work together it is doable. The mechanisms exist and the technology exists."

If a deal is done, the first inspectors to land in Damascus are likely to be drawn from the multinational roster of 126 working for the Organisation for the Prohibition of Chemical Weapons (OPCW).

The Hague-based agency is little known compared with its nuclear cousin, the International Atomic Energy Agency, but in its 16 years, it has overseen the destruction of more than 70,000 tons of chemical weapons in seven countries, eliminating the entire arsenals of Albania, South Korea and India, and almost the whole stockpiles of the US and Libya. The vast Russian arsenal inherited from the Soviet Union is about two-thirds destroyed.

Syria is due to become a state party to the CWC on 11 October, 30 days after the president sent his application letter to the UN on Thursday. Syria would then be legally bound by the convention prohibiting production, stockpiling or use of chemical weapons.

The government in Damascus would then have another 30 days (the US and its allies will argue for an accelerated timetable) to produce a full declaration of all its chemical agents, both in weapons and in bulk storage, as well as precursor chemicals, production facilities and delivery systems. It is that declaration that the OPCW inspectors would take to Damascus.

From the airport, they would fan out under military guard to the chemical weapon sites. Alongside its declaration the regime would have to provide a detailed plan for getting inspectors safely to the sites. As the most significant of these locations are expected to be army bases in regime-controlled territory, this initial mission will not involve crossing front lines and should therefore not be as precarious as the last Damascus mission. But the risks would still be substantial.

"The big problem for the OPCW is to what extent are they going to risk the lives of their inspectors to monitor the process," Zanders said. "The security guarantees are going to be paramount."

Once on site, the inspectors would draw up an inventory, counting canisters of nerve agents and precursor chemicals, as well as shells, rockets and aerial bombs with chemical payloads. Every item would be assigned a barcode and a seal would be attached that would sound an alert if tampered with. The inspectors would set up cameras to monitor the site remotely.

At that point – possibly well before the end of the year – at least some of the Syrian arsenal would be under international control, in the sense in that the OPCW and its member states would know if the weapons were moved or used.

"Once everything is inventoried and sealed you can give a sigh of relief," said Matthew Meselson, a chemical and biological arms expert at Harvard University. "Demilitarisation will be a long-term process after that, but in the first few weeks you will have broken the back of the problem, because once anyone tried to take the weapons there would be a big international reaction."

Two huge challenges would remain. The international community would have to check whether the Syrian declaration was complete, a process that the Iraqi experience suggests could take years. Second, there would be the long process of destruction.

Paradoxically, the CWC has made it harder to get rid of chemical weapons. Before it came into effect in 1997, munitions were often tossed into the sea. Baltic fisherman and Polish holidaymakers are still being burned by the thousands of mustard gas shells Britain, Germany and the Soviet Union dumped in the Gotland Deep after the second world war.

The improvised methods used in Iraq in 1991, blowing up and burning chemical bombs in deep pits, are also not allowed under the CWC for environmental reasons. Nor is the shipping of chemical munitions or agents outside state borders.

There are now two major strategies for destroying munitions that are filled with chemical agents. The first is cold detonation. Here, the munition is surrounded with explosives – and sometimes water bags – and put in an armor-plated blast chamber, or "bang box".

On detonation, the explosion destroys the munition and the agent inside. The water bags absorb some of the blast and fill the chamber with steam, which helps break down any residual agent. The waste is pumped through filters, oxidizers and beds of carbon to remove acidic and organic vapours, soot and dust. The system has been tested at Britain's Porton Down facility and no agent vapors were found in the vented gas. A large system can handle about 40 munitions in 10 hours. It is transported on eight 40ft trailers.

The second approach is hot detonation. The munitions are place in a kiln at 600C. The munition explodes in the heat and waste gases are held inside long enough to break them down or sent through filters and scrubbers to clean them. The system was used to destroy 16 tons of mustard gas the Albanian government found in 1997 left over from the communist era. The process took about six months but almost began in tragedy when the first canister incinerated in 19 seconds instead of the 19 minutes expected, blowing out the bottom of the containment vessel. But the method has been refined somewhat since then. The Swedish company, Dynasafe, has a mobile version that is carried on three flatbed trailers.

Bulk stores of chemical agents that have not been loaded into weapons are simpler to deal with. Most of the US stockpile of chemical weapons has been destroyed with incineration. The intense heat and air oxidizes the chemical agents into carbon dioxide and water, though amounts of nasty chemicals remain, such as furans and dioxins, which have to be filtered out. Other liquid and solid waste can be sent to a commercial hazardous waste treatment plant. Portable incinerators have been built, but rarely deployed.

Neutralization, the cheaper process favored by the Russians, uses water and chemicals to convert warfare agents into more benign substances. This was used to destroy nerve agents, including tabun and sarin, at production facilities in Iraq in the early 1990s. The Iraq plant processed more than a ton of chemicals per day, but the waste contained sodium cyanide and had to be stored in steel tanks sealed in concrete bunkers. The US has built what it calls a field deployable hydrolysis system, which can be flown to a site and made ready within 10 days. Inside a titanium tank, chemical agents are mixed with water, sodium hydroxide and other chemicals, then heated to split them apart. The facility can process about 25 tons of agent a day.

With such new portable technology, the bulk of the Syrian arsenal could conceivably be destroyed within a year, so long as it were possible to move the weapons safely to a handful of sites that could be kept secure.

But Ralf Trapp, a German former OPCW official, believes the task is worth starting, even if its completion appears distant. "All parties would have to work together to come up with arrangements, and that is a positive thing," Trapp said. "The alternative is to leave the stuff alone, and that is almost an invitation to use it again."

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