The Americans and their allies have long been waging a war of the shadows against the Islamic Republic, with Tehran often giving as good as it gets.
On May 24, Abdolhamid Rigi, a senior commander of the largest insurgent group in Iran, Jundallah, was hanged for masterminding bombings and the murder of government officials.
His group, Jundallah, or Soldiers of God, operates in southeastern Sistan-Baluchistan province, which is predominantly Sunni Muslim.
Tehran claims it is armed and funded by the U.S. Central Intelligence Agency, Israel's Mossad intelligence service and Britain's Secret Intelligence Service known as MI6.
Jundallah has twice tried to assassinate hard-line President Mahmoud Ahmadinejad. It is one of several rebel groups along Iran's periphery that are fighting the Tehran regime seeking independence or autonomy from the Shiite-dominated state.
In February, Iranian intelligence agents captured Rigi brother, Abdulmalik, Jundallah's supreme leader and the group's founder.
That was a major blow to the organization and it is likely that the Americans will seek to rebuild the group as U.S. clandestine operations are stepped up.
Four Kurdish rebels were executed in Tehran's notorious Evin Prison May 9 for attacks against the state. All belonged to a separatist group called the Party of Free Life of Kurdistan based in the Kurdish provinces of Western Iran along the border with Iraq.
The Americans and Israel are reported to be active with the Kurds.
Expanding the U.S. military's undercover operations in regions where al-Qaida and its allies are most active means that Special Forces troops will be conducting missions that have long been the preserve of the CIA and other civilian organizations.
The Department of Defense has wider latitude than the CIA when it comes to such activity, and the shift toward covert military operations is likely to intensify the rivalry between Langley and the Pentagon.
Unlike the CIA, military operations of this nature do not require presidential approval or regular reports to Congress.
The secret directive came to light with a May 24 New York Times report that said the order was signed Sept. 30, 2009, by Gen. David Petraeus, head of the U.S. Central Command.
Officials stressed that the directive, the Joint Unconventional Warfare Task Force Execute Order, permits operations that could pave the way toward possible military attacks against Iran if the confrontation over Tehran's nuclear program worsens.
To what extent the military will employ private security companies, largely staffed with ex-military men and ex-CIA operatives, in these missions is not clear.
But U.S. officials say military commanders continue to maintain a secret network of private spies deep inside Pakistan and Afghanistan despite widespread concerns about what is seen by many as a rogue operation that could backfire with potentially dangerous consequences.
The New York Times has reported that the exhaustive reports these agents have provided on al-Qaida and the Taliban "have become an important source of intelligence" for U.S. commanders.
On May 3, Raja News, a conservative Iranian media outlet, reported that U.S security company Xe Services, formerly known as Blackwater, which became notorious for its actions in Iraq, is working with Iranian dissidents of the Mujahedeen-e Khalq, or People's Holy Warriors, for intelligence-gathering and sabotage operations inside Iran.
Given the murky nature of intelligence work, that is not beyond the bounds of possibility, even though Washington lists the group as a terrorist organization.
The MeK was for years the only rebel group fighting the Tehran regime. Its military wing was based in Iraq from the mid-1980s until the fall of Saddam Hussein's regime in March 2003.
It was widely believed the CIA employed a significant number of MeK operatives for intelligence missions inside Iran.
U.S.-based global intelligence consultancy Stratfor has dismissed the Raja News report as "likely an exaggeration, if not an outright fabrication, crafted to serve domestic Iranian political interests."
It concluded that naming the MeK, which is widely hated inside Iran, and Xe, reviled for reckless operations that killed Iraqi civilians, was intended "to shape perceptions among Iranian policymakers" who may be inclined toward a rapprochement with the United States.
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