MC1(AW) Nathanael Miller / U.S. Navy The destroyer USS Barry, currently steaming in the Mediterranean Sea awaiting possible orders to attack Syria with Tomahawk cruise missiles, launches one against Libya on Mar. 19, 2011.

Taking out Syria’s chemical-weapons stockpile isn’t easy – and is fraught with perils, including creating plumes of deadly vapors that could kill civilians downwind of such attacks.

That’s why Pentagon officials suggest that any U.S. and allied military strike against Syria will tilt toward military, and command and control, targets —including artillery and missile units that could be used to launch chemical weapons — instead of the bunkers believed to contain them.

Secretary of State John Kerry made clear Monday that military action is all but inevitable in the coming days. “We know that the Syrian regime maintains custody of these chemical weapons. We know that the Syrian regime has the capacity to do this with rockets,” he said. “President Obama believes there must be accountability for those who would use the world’s most heinous weapons against the world’s most vulnerable people.”

But targeting the weapons themselves may not make the most military sense.

For starters, neither the U.S. nor its allies know where Syrian dictator Bashar al-Assad is keeping his cache of hundreds of tons of sarin, mustard gas and other chemical agents. That means that any military strike to take them out will surely leave some untouched.

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After more than two years of civil war, the Syrian military has distributed many of its chemical arms beyond the original 15 or so major storage sites where Western intelligence agencies believe they were housed when the conflict began. “Dispersing the stuff would make [attacking it] more difficult,” says Eliot Cohen, a former Pentagon official now at the Johns Hopkins University’s School of Advanced International Studies in Washington. Blowing up storage sites, he warns, also could “leave the facilities so shattered that people can come in and pick the stuff up that you don’t want them to pick up.”

Secondly, the Obama Administration and its allies aren’t considering deploying troops to seize and secure such weapons. The Pentagon has estimated that mission could take 75,000 troops.

Last month, Army General Martin Dempsey, chairman of the Joint Chiefs of Staff, detailed for Senator Carl Levin, the Michigan Democrat who chairs the armed services committee, the difficulties associated with using military force to seize control of Syria’s chemical stockpile.

“We do this by destroying portions of Syria’s massive stockpile, interdicting its movement and delivery, or by seizing and securing program components,” he said in his July 19 letter assessing U.S. military options in Syria. “At a minimum, this option would call for a no-fly zone as well as air and missile strikes involving hundreds of aircraft, ships, submarines, and other enablers. Thousands of special operations forces and other ground forces would be needed to assault and secure critical sites.”

Neither the nation—nor President Obama—has any desire for U.S. combat boots on Syrian soil. So U.S. defense officials are weighing air strikes to punish Assad’s government for their suspected use of chemical weapons. But because the Pentagon doesn’t want to put primarily U.S. pilots at risk of being shot down and held hostage by Damascus, it’s leaning toward the use of Tomahawk Land Attack Missiles—TLAMs—against Syrian targets.

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Unfortunately for U.S. war planners, Tomahawk cruise missiles pack a relatively puny 1,000-pound warhead. That’s unlikely to punch through buried chemical-weapons bunkers and generate the intense, sustained heat needed to incinerate sarin or other chemical weapons inside.

“Doing this with Tomahawks is going to be a challenge,” says Amy Smithson, a chemical-weapons expert at the James Martin Center for Nonproliferation Studies in Washington. “You may get half of them with Tomahawks, but I have plume concerns—anybody in the neighborhood is going to be in big, bad trouble” if the poisonous agents drift their way.

Bulk chemicals not already loaded into individual shells are especially vulnerable to being spread by bombing. That’s why Smithson believes that Western governments should provide those near targeted chemical-storage sites with protective gear before launching any attacks. “Syrian civilians and rebel forces,” she says, “could benefit greatly from gas masks.”

Dempsey, the chairman of the Joint Chiefs, sketched out a likely U.S. military response to Syria’s use of chemical weapons in that July letter to Levin. He termed it Conduct Limited Stand-off Strikes:

This option uses lethal force to strike targets that enable the regime to conduct military operations, proliferate advanced weapons, and defend itself. Potential targets include high-value regime air defense, air, ground, missile, and naval forces as well as the supporting military facilities and command nodes. Stand-off air and missile systems could be used to strike hundreds of targets at a tempo of our choosing.

Cohen is leery of a tit-for-tat strike that he fears the Obama Administration is considering. The apparent indiscriminate use of deadly agents against civilians, he argues, requires a disproportionate response by the U.S. to convince other states from doing the same.

“You want people to understand that, if you do this, you lose your war,” Cohen says. The Obama Administration should consider destroying Syria’s air force, its air defenses, and many of its airfields to retaliate if Syria’s use of chemical weapons is confirmed. “The objective,” he argues, “should be crippling the regime.”

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