Turkey is alarmed by extremist militants in Syria border area

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A wounded Syrian woman walks with her children after airstrikes on a rebel area of the war-torn northern city of Aleppo. (Mohammed al-Khatieb / AFP/ Getty Images)

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Mourners attend a funeral for men killed during battles with members of the Al Qaeda-linked Islamic State of Iraq and Syria in the northern Syrian city of Aleppo. (Mahmud Al-Halabi / AFP/ Getty Images)

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Rebel fighters carry a man’s body at the Aleppo headquarters of the Islamic State of Iraq and Syria after he was allegedly killed by the AlQaeda-linked group in January. (Medo Halab / AFP/ Getty Images)

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A Syrian man helps an injured resident following an airstrike in Aleppo’s Maadi neighborhood. (Mohammed al-Khatieb / AFP/ Getty Images)

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A Syrian man reacts after an airstrike by government forces on the city of Aleppo. (Mohammed al-Khatieb / AFP/ Getty Images)

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Rebel fighters inside a building during clashes with pro-government forces in the Sheikh al-Said neighborhood of Syria’s northern city of Aleppo. (Medo Halab / AFP/ Getty Images)

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An opposition fighter runs through a hole in a wall to avoid sniper fire by regime forces during clashes in Syria’s northern city of Aleppo. (KARAM AL-MASRI / AFP/Getty Images)

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Opposition fighters open fire from behind a car during fighting in the Salaheddin district of the northern Syrian city of Aleppo. The Syrian Observatory for Human Rights reported fierce fighting in Damascus province between rebels and troops backed by pro-regime militias and fighters from Lebanon’s Shiite Muslim movement Hezbollah. (KARAM AL-MASRI / AFP/Getty Images)

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A Syrian rebel aims his weapon during clashes with government forces in the streets near Aleppo international airport in northern Syria. (Stephen J. Boitano / AFP/ Getty Images)

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Rebel fighters duck as they run behind a barricade to avoid being fired at by Syrian government forces in the Old City of Aleppo. (JM Lopez / AFP/ Getty Images)

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A fighter allied with Syrian President Bashar Assad runs across the street after fighting with rebels in the Yarmouk refugee camp in the capital, Damascus. (Anwar Amro / AFP/ Getty Images)

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A fighter of the Popular Front for the Liberation of Palestine General Command, allied with Syrian President Bashar Assad, jumps through the window of a destroyed building in the Yarmouk refugee camp in Damascus. (Anwar Amro / AFP/ Getty Images)

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An opposition fighter runs in front of a sniper curtain in the industrial area of Syria’s eastern town of Deir Ezzor during clashes with government forces. (Abo Shuja / AFP/ Getty Images)

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Free Syrian Army fighters clean their weapons and check ammunition at their base on the outskirts of Aleppo, Syria. (Khalil Hamra / Associated Press)

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Syrian government forces patrol the Khaldiyeh district of Syria’s central city of Homs. The Syrian government announced on July 29 the capture of Khaldiyeh, a key rebel district in Homs. (Joseph Eid / AFP/Getty Images)

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A Syrian national flag is waved in Damascus to show support for President Bashar Assad. (Louai Beshara / AFP/Getty Images)

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A rebel fighter takes aim at regime forces in the northern Syrian city of Aleppo. (Louai Abo Al-Jod / AFP/Getty Images)

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A man stands near destroyed buildings after reported airstrikes by Syrian government forces in the rebel-held northwestern Syrian province of Idlib. (Abu Amar Al-Taftanaz / AFP/Getty Images)

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Mustafa Abu Bekir, 23, second from left, meets relatives after crossing the Turkish Cilvegozu gate border. Abu Bekir said he was severely wounded by a bomb dropped from a Syrian army warplane while fighting with the Free Syrian Army in Idlib. (Gregorio Borgia / Associated Press)

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A man carries a boy who was severely wounded during heavy fighting between Syrian rebels and troops last year in Idlib. (Rodrigo Abd / Associated Press)

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Syrian President Bashar Assad arrives at a dinner event in Damascus on the last week of the Muslim holy month of Ramadan. (Virginie Nguyen Hoang / AFP/Getty Images)

By Patrick J. McDonnell

Nov. 10, 2013 9 AM PT

REYHANLI, Turkey — In this bustling border town, anonymous apartments serve as safe houses for Syrian rebel commanders, clinics for wounded fighters and opposition media centers equipped with banks of sophisticated laptops and video gear.

Turkey has allowed an assemblage of Syrian rebels and their associates, including secular activists, cash-wielding sheiks, arms traffickers and Islamist militants, to use its territory as a transit route, logistics hub and rest stop.

The government has been very clear that it wants to see Syrian President Bashar Assad removed from power. But after more than two years, the conflict is dragging on. Al Qaeda-linked rebel groups are strengthening rapidly in Syria and seizing territory close to the Turkish frontier, the eastern boundary of the NATO alliance.

Increasingly, officials in Ankara, the Turkish capital, as well as critics of the government’s policy worry that the militants will establish a permanent presence, exporting extremist ideas and fighters from a chaotic, war-torn state. Despite concern in Washington about the militants’ advance, Turkey appears to have few good options.

“Ankara’s calculation has been that Assad has to go, and Turkey will allow anyone who wants to fight Assad to go into Syria,” said Soner Cagaptay, an analyst with the Washington Institute for Near East Policy. “To Turkey it didn’t matter that much if there were some bad guys, because once Assad was gone the good guys would take over and clean out the bad guys.”

Now that calculus is changing. “Turkey is realizing that Assad may not go,” Cagaptay said. “And the good guys may not take over.”

Turkish artillery batteries opened fire last month on positions in Syria of a powerful Al Qaeda-linked rebel faction, the Islamic State of Iraq and Syria, after its fighters captured the Syrian town of Azaz, just three miles from the border. Turkey shut the crossing to Azaz, prompting an Internet threat by the group to extend a campaign of car bombings to Turkish soil.

Turkey could be more cautious about which Syrian opposition groups receive aid and who can operate in the border region. Officials are pushing back against charges that Turkish territory has become a launch pad for Al Qaeda-linked groups such as Al Nusra Front. News reports have cited seizures of trucks carrying what they described as suspicious chemicals and warheads for hundreds of rockets.

But sealing the frontier zone to Syrian rebel factions would choke off supply routes and could lead to the collapse of the entire anti-Assad rebellion in Syria’s north.

Alarmed by the downward spiral, Turkey has launched something of a diplomatic offensive with neighbors, including Iran, a key backer of the Assad government. Iran’s foreign minister, Mohammad Javad Zarif, visited Ankara early this month and the two nations vowed to work together to find a solution for Syria, despite being on opposite sides of a proxy war there.

When an armed rebellion first surfaced against the autocratic Assad in 2011, Turkish officials embraced a vigorous policy of backing the opposition on the assumption that Assad’s government was on the verge of collapse. Assad’s exit would have opened the way for Turkey’s grateful clients to seize power in Damascus.

But it hasn’t worked out that way, with Assad clinging to power as the West, and most specifically the Obama administration, opted not to provide robust military aid to the Syrian opposition.

Turkish Prime Minister Recep Tayyip Erdogan, architect of Ankara’s Syria policy, did not hide his displeasure when the recent U.S.-Russian-brokered deal to neutralize Syria’s chemical weapons seemed to rule out the prospect of an American bombing campaign against Syria.

Erdogan rejects the idea that Islamic militant groups could gain a foothold in Turkey. “It is out of the question that organizations like Al Qaeda or Al Nusra could take shelter in our country,” he said Thursday on a visit to Sweden.

But his policy of providing a welcome mat for Syrian rebels of all stripes is drawing the ire of many Turks who fear that long-secular Turkey is being dragged into Syria’s increasingly sectarian quagmire.

“Why are we bringing in all these crazies here?” asked Suleyman Osterek, an opposition politician in Antakya, another border-area town that has seen an influx of Syrian fighters. “These people scare us.”

In an interview this month with Britain’s Guardian newspaper, Turkish President Abdullah Gul voiced concern that Syria could become “something like Afghanistan on the shores of the Mediterranean.”

It is unclear whether additional Western military support or even direct U.S. intervention would have pushed Assad out or just accelerated the process of militarization and radicalization in Syria. Afghanistan in the 1980s, Iraq after the 2003 U.S.-led invasion and current-day Libya all provide examples of Islamist militants gaining traction after the West-backed toppling of authoritarian governments.

Today, fractious opposition brigades and sundry warlords hold sway over vast stretches of Syria. The Islamic State of Iraq and Syria and another Islamist offshoot, Al Nusra Front, both apparently bankrolled by wealthy donors in the Persian Gulf and elsewhere, now count among insurgent Syria’s major power brokers, and by some accounts are the most dominant.

The Islamic State has drawn thousands of recruits from other rebel units and throngs of eager volunteers from dozens of nations. Turkey is now widely regarded as a transit route for Syria-bound Islamist militants from the Persian Gulf, North Africa, Europe and Chechnya and elsewhere. Iraqi, Jordanian and Lebanese volunteers usually enter via their nations’ borders with Syria, experts say.

With extremists in the ascendance, the U.S.-backed policy of aiding “moderate” rebel groups appears to face major hurdles.

The numbers of foreign Islamist militants in Syria now exceed those who previously flocked to Iraq and Afghanistan, according to U.S. congressional estimates. There is widespread concern in the West that the Syrian conflict is incubating a new generation of extremists who could eventually wreak havoc across the globe.

“When it is over, these people will be combat trained, combat hardened, and they are going to want to go home,” U.S. Rep. Mike Rogers (R-Mich.), chairman of the House Intelligence Committee, said last month.

As Turkey grapples with the Islamist militants on its doorstep, it also faces the emergence in northern Syria of autonomy-minded Kurdish militiamen allied with the Kurdistan Workers Party. Turkey has battled the party for more than 30 years, though peace talks are now underway.

Secular Kurdish militiamen, who have long viewed the radical Islamist forces as their archenemy, have proved to be the sole Syrian faction capable of pushing back the onslaught. Late last month, Kurdish militiamen overran a crossing along the Iraqi border, expelling Al Qaeda-affiliated fighters.

The volatile border tableau has prompted speculation that Ankara could eventually seek a strategic alliance with Syrian Kurds. Though improbable on one level, it no longer seems out of the question, analysts say.

“Turkey is going to have to make some very, very difficult decisions, given the way Syria has unraveled,” said Howard Eissenstat, a Turkey expert at St. Lawrence University in New York. “They are backing up, recalibrating and saying, ‘OK, what is our long game going to look like?’”

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Special correspondent Nabih Bulos contributed to this report.