Since 9/11, the overriding concern of U.S. policy across the Middle East and Central Asia has been to defeat al-Qaida and other radical Islamic groups. Hundreds of billions of dollars are being spent on that obsession. Yet when the secret history of the current “Arab Spring” is written, we may learn that one of the many unintended consequences of U.S. attempts to keep up with — and influence — the historic events was to provide a flood of new recruits to radical Islam.

The immediate cause: Saudi intervention in Bahrain.

While America and its allies have launched a military effort to protect the rebels in Libya, the Obama administration has voiced only muted protests as its major Arab ally in the region, Saudi Arabia, crushes the rebels in Bahrain — with what could be ruinous reverberations for all concerned.

The rebels in Bahrain are predominately Shiites who have long chafed under minority Sunni rule. Riding a surging wave of popular protests, the Shiites seemed to be on the road to forcing the government in Manama to accept at least some of their demands.

With the U.S. 5th Fleet based in Bahrain, American officials have also been concerned about the unrest. But their attempts to encourage the government to meet some basic demands for change failed. U.S. Defense Secretary Robert Gates, visiting Manama on March 12, criticized the regime for its “baby steps” toward reform.

Meanwhile, King Abdullah in neighboring Saudi Arabia looked on with horror as the Arab Spring came sweeping toward him. The Saudi elite, Sunnis themselves, have their own restive Shiite minority to contend with. The king was also concerned that a Shiite breakthrough in Bahrain would strengthen Iran’s sway in the region.

Even more alarming for Abdullah was the alacrity with which President Barack Obama turned his back on one-time dictator allies. America’s unceremonious dumping of Egypt’s Hosni Mubarak was a shocking harbinger. Could Washington’s remaining key Arab ally be next?

Thus, on March 14, the Saudis (along with their Persian Gulf allies) finally acted. They dispatched a thousand troops along with tanks and armored vehicles across the causeway that separates them from Bahrain to help brutally stifle the revolt.

In the process, the Saudi king reportedly ignored a specific request from Obama to stay out. The hell with the duplicitous Americans! He’d had enough of following Washington’s lead. The Americans were shocked and humiliated. Relations between the two governments are supposedly at a nadir.

That’s the official version. But when the history of these events is written, I imagine the real facts will tell a more Machiavellian tale: that the U.S. in fact gave a tacit go-ahead to the Saudis to act — with disastrous results.

There have been some unconfirmed reports to that effect, and they make sense. There was a trade-off: Libya for Bahrain. Without the Saudis, the U.S. could never have convinced the Arab League to ask for the creation of a no-fly zone over Libya. And without that Arab League resolution, the intervention in Libya would never have occurred. The Saudis and their Gulf partners are also taking part to some extent in that intervention, to provide at least a façade of Arab participation.

In return, I suspect, U.S. officials have been very muted in any criticism of the brutal crackdown in Bahrain — a country much more vital to Saudi interests than is Libya.

And brutal it has been: Backed up by the Saudis, Bahraini security forces and pro-regime thugs armed with swords and clubs attacked demonstrators throughout the kingdom. Human rights activists reported that 26 people have been killed, 300 have been imprisoned, and at least 35 people are missing in the three weeks since the crackdown began in earnest.

Yet scarcely a peep out of Washington.

OK, you say. What’s wrong with the U.S. trading Bahrain for Libya? It’s realpolitik, right out of the Henry Kissinger playbook.

Except that the consequences of that Saudi intervention may prove much more disastrous to Western (and Saudi) interests than any possible positive fallout from the adventure in Libya.

That according to a study just issued by the International Crisis Group. What has happened, says the report, is that the now thwarted and bloodied Shiite protesters in Bahrain, who had thought they could achieve change through peaceful protests — as the Americans have been advocating — may now turn to violence — exactly as al-Qaida and other radical Islamic groups have been preaching.

As the report puts it, “Manama’s crackdown and Saudi Arabia’s military intervention are dangerous moves that could stamp out hopes for peaceful transition in Bahrain and turn a mass movement for democratic reform into an armed conflict, while regionalizing an internal political struggle. They could also exacerbate sectarian tensions not only in Bahrain or the Gulf but across the region.

“Along with other member states of the Gulf Cooperation Council (GCC), Saudi Arabia purportedly is responding to dual fears: that the takeover would be tantamount to an Iranian one. Both are largely unfounded. It also is concerned protests might inspire similar movements among its own Eastern Province Shiites, oblivious that its involvement is likelier to provoke than deter them.

“Bahrain’s brutal crackdown and Saudi interference fan flames both want to extinguish. The most effective response to the radical regime change threat or greater Iranian influence is not violent suppression of peaceful protests but political reform. Time is running short and trends are in the wrong direction.

“In short, the intervention likely achieved precisely the opposite of what it intended.”

Over the years, throughout the region, from Egypt to Yemen to Saudi Arabia, such repression and subsequent radicalization has been a vital source of recruits for al-Qaida.

Yet, on his latest visit to Saudi Arabia, Gates, secretary of defense of what is still billed as the most powerful nation on the planet, reportedly didn’t dare raise the issue of Bahrain with King Abdullah.

Just imagine having to face the monarch’s wrath!

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