Israel has long used assassination against its enemies, "hoping that by taking out individuals, they can alter, change the course of history," says Ronen Bergman, an Israeli commentator and author of "Israel's Secret War with Iran" and an upcoming book tentatively titled "Mossad and the Art of Assassination."

Bergman said the attacks have three purposes, the most obvious being the removal of high-ranking scientists and their  knowledge. The others:  forcing Iran to increase security for its scientists and facilities and to spur “white defections.”

He explained the latter this way: “Scientists leaving the project, afraid that they are going to be next on the assassination list, and say, ‘We don't want this.  Indeed, we get good money, we are promoted, we are honored by everybody, but we might get killed.  It isn't worth it.  Maybe we should go back to teach … in a university.’”

There are unconfirmed reports in the Israeli press and elsewhere that Israel and the MEK were involved in a Nov. 12 explosion that destroyed the Iranian missile research and development site at Bin Kaneh, 30 miles outside Tehran.  Among those killed was Maj. Gen. Hassan Moghaddam, director of missile development for the Revolutionary Guard, and a dozen other researchers. So important was Moghaddam that Ayatollah Khamenei attended his funeral.

Unlike the assassinations, Iran claims the missile site explosion was an accident; the MEK, meanwhile, trumpeted it but denied any involvement.

Indeed, there may be other covert operations carried out either by Israel acting alone or in concert with others, according to Bergman.

“Two labs caught fire,” said Bergman, enumerating the attacks. “Scientists got blown up or disappeared.  A missile base and the R&D base of the Revolutionary Guard exploded some time ago, with the director of the R&D division of the Revolutionary Guard being killed along with … his soldiers.”

Bergman added, “So, a long series of … something that was termed by an Israeli (Cabinet) minister … as ‘mysterious mishaps’ happening and rehappening to the project. Then the Iranians claim, ‘This is Israeli Mossad trying to sabotage our attempts to be a nuclear superpower.’”

Dr. Uzi Rabi, director of the Dayan Center at Tel Aviv University, said the supposed accidents could all be part of “psychological warfare” conducted against Iran. “It seems logical. It makes sense,” he said of possible MEK involvement, “and it’s been done before.”

Rabi, who regularly briefs Israel’s parliament, the Knesset, on Iran also said the ultimate goal of the range of covert operations being carried out by Israel is “to damage the politics of survivability … to send a message that could strike fear into the rulers of Iran.”

For the United States, the alleged role of the MEK is particularly troublesome.  In 1997, the State Department designated it a terrorist group, justifying it with an unclassified 40-page summary of the organization’s  activities going back more than 25 years.  The paper, sent to Congress in 1998, was written by Wendy Sherman, now undersecretary of state for political affairs and then an aide to Secretary of State Madeleine Albright.

The report, which was obtained by NBC News, was unsparing in its assessment. “The Mujahedin  (MEK) collaborated with Ayatollah Khomeini to overthrow the former shah of Iran,” it said. “As part of that struggle, they assassinated at least six American citizens, supported the takeover of the U.S. embassy, and opposed the release of the American hostages.”  In each case, the paper noted, “Bombs were the Mujahedin's weapon of choice, which they frequently employed against American targets.”

“In the post-revolutionary political chaos, however, the Mujahedin lost political power to Iran's Islamic clergy. They then applied their dedication to armed struggle and the use of propaganda against the new Iranian government, launching a violent and polemical cycle of attack and reprisal."

U.S. officials have said publicly that the information contained in the report was limited to unclassified material, but that it also drew on classified material in making its determination to add the MEK to the U.S. list of terrorist organizations.

Sean Gallup / Getty Images file

Maryam Rajavi, president of the National Council of Resistance of Iran

The MEK and its sister organizations have since the beginning been run by Massoud and Maryam Rajavi, a husband-wife team who have maintained tight control despite assassination threats and internal dissent. Massoud Rajavi, 63, founded the MEK, but since the U.S. invasion of Iraq has taken a backseat to his wife.

The State Department report describes the Rajavis as  “fundamentally undemocratic” and “not a viable alternative to the current government of Iran.”

One reason for that is the MEK’s close relationship with Saddam Hussein, as demonstrated by this 1986 video showing the late Iraqi dictator meeting with Massoud Rajavi. Saddam recruited the MEK in much the same way the Israelis allegedly have, using them to fight Iranian forces during the Iran-Iraq War, a role they took on proudly.  So proudly, they invited NBC News to one of their military camps outside Baghdad in 1993.

“The National Liberation Army (MLA), the military wing of the Mujahedin, conducted raids into Iran during the latter years of the 1980-88 Iran-Iraq War,” according to the State Department report. The NLA's last major offensive reportedly was conducted against Iraqi Kurds in 1991, when it joined Saddam Hussein's brutal repression of the Kurdish rebellion. In addition to occasional acts of sabotage, the Mujahedin are responsible for violent attacks in Iran that victimize civilians.”

“Internally, the Mujahedin run their organization autocratically, suppressing dissent and eschewing tolerance of differing viewpoints,” it said. “Rajavi, who heads the Mojahedin’s political and military wings, has fostered a cult of personality around himself.”

The U.S. suspicion of the MEK doesn’t end there. Law enforcement officials have told NBC News that in 1994, the MEK made a pact with terrorist Ramzi Yousef a year after he masterminded the first attack on the World Trade Center in New York City.  According to the officials, who spoke on condition of anonymity, Yousef built an 11-pound bomb that MEK agents placed inside one of Shia Islam’s greatest shrines in Mashad, Iran, on June 20, 1994. At least 26 people, mostly women and children, were killed and 200 wounded in the attack.

That connection between Yousef, nephew of 9-11 mastermind Khalid Sheikh Mohammad, and the MEK was first reported in a book, “The New Jackals,” by Simon Reeve. NBC News confirmed that Yousef told U.S. law enforcement that he had worked with the MEK on the bombing.

In recent years, the MEK has said it has renounced violence, but Iranian officials say that is not true, that killings of Iranians continue.  Still, through some deft lobbying, the group has been able to get the United Kingdom and the European Union to remove it from their lists of terrorist groups.

The alleged involvement of the MEK in the assassinations of Iranian nuclear scientists provides the U.S. with a cloak of deniability regarding the clandestine killings. Because the U.S. has designated the MEK as a terrorist organization, neither military nor intelligence units of the U.S. government, can work with them.  “We cannot deal with them, “ said one senior U.S. official. “We would not deal with them because of the designation.”

Iranian officials initially accused the Israelis and MEK of being behind the attacks, but they have since added the CIA to the list. Three days after the Jan. 11, 2012, bombing in Tehran that killed Roshan, the state news agency IRNA reported that Iran’s Foreign Ministry had sent a diplomatic letter to the U.S. claiming to have “evidence and reliable information” that the CIA provided “guidance, support and planning” to assassins directly involved in the attack.

U.S. Secretary of State Hillary Clinton  immediately denied any connection to the killings. “I want to categorically deny any United States involvement in any kind of act of violence inside Iran,” Clinton told reporters on the day of the attack.

But at least two GOP presidential candidates have no problem with the targeting of nuclear scientists.  In a November debate, former House Speaker Newt Gingrich endorsed “taking out their scientists,” and former Pennsylvania Sen. Rick Santorum called it, ”a wonderful thing.”

The MEK’s opposition to the Iranian government also has recently earned it both plaudits and support from an odd mix of political bedfellows.

A group of former Cabinet-level officials have joined together to support the MEK’s removal from the official U.S. Foreign Terrorist Organization list, even taking out a full-page ad last year in the New York Times calling for the removal of the MEK from the U.S. terrorist list.  Former Vermont Gov. Howard Dean, former U.S. Attorney General Michael Mukasey, former U.N. Ambassador John Bolton; former Homeland Security Secretary Tom Ridge, former FBI Director Louis Freeh and former Rep. Patrick Kennedy were among those whose signatures were on the ad.

“There’s an extraordinary group of bipartisan or even apolitical leaders, military leaders, diplomats, the United States … the United Kingdom, the European Union, even a U.S. District Court in Washington, said that this group that was put on the foreign terrorist organization watch list in 1997 doesn’t deserve to be there,” Ridge said in November on “The Andrea Mitchell Show” on MSNBC TV.

U.S. politicians also have been pushing the U.S. government to protect the 3,400 MEK members and their families at Camp Ashraf in Iraq, about 35 miles north of Baghdad.  With the departure of U.S. troops, the MEK feared that Iraqi forces, with encouragement from Iran, would attack the camp, leading to a bloodbath. At the last minute, however, agreement was brokered with the United Nations that would permit the MEK members’ departure for resettlement in unspecified democratic countries. As of this week, there’s been little movement on the planned resettlement.

Jassim Mohammed / AP file

Iranian fighters with the National Liberation Army, the military wing of the MEK, clean armored personnel carriers in 1997 after a field exercise near Camp Ashraf in Iraq.

The Iranians see what’s happening as terrorism and hypocrisy by the United States.  They have forwarded documents and other evidence to the United Nations – and directly to the United States, they say.

“I think this is very cynical plan.  This is unacceptable,” said Larijani. “This is a bad trend in the world.  Unprecedented.  We should kill scientists … to block a scientific program?  I mean this is disaster!”

Daniel Byman, a professor in the School of Foreign Service at Georgetown University and also a senior fellow with the Saban Center for Middle East Policy at the Brookings Institution, said that if the accounts of the Israeli-MEK assassinations are accurate, the operation borders on terrorism.

“In theory, states cannot be terrorist, but if they hire locals to do assassinations, that would be state sponsorship,” said Byman, author of the recent book, “A High Price: The Triumphs and Failures of Israeli Counterterrorism.” “You could argue that they took action not to terrorize the public, the purpose of terrorism, but only the nuclear community.  An argument could also be made that degrading the program means that you don’t have to take military action and thus, this is a lower level of violence and that really these are military targets, where normally terrorist targets are civilians.”

But ultimately, Byman said, there is a “spectrum of responsibility” and that Israel is ultimately responsible.

Ronen Bergman, while not speaking on behalf of the Israeli government, suggests that there is a justification, citing an oft-repeated but disputed quote in which Iranian President Mahmoud Ahmadinejad’s said that Israel should be wiped off the face of the earth.

“Meir Degan, the chief of Mossad, when he was in office, hung a photograph behind him, behind the chair of the chief of Mossad,” notes the Israeli commentator.  “And in that photograph you see -- an ultra-orthodox Jew -- long beard, standing on his knees with his-- hands up in the air, and two Gestapo soldiers standing -- beside him with guns pointed at him.  One of -- one of them is smiling.

“And Degan used to say to his people and the people coming to visit him from CIA, NSA, et cetera, ‘Look at this guy in the picture. This is my grandfather just seconds before he was killed by the SS,’” Bergman said. “’… We are here to prevent this from happening again.’"

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Richard Engel is NBC News' chief foreign correspondent; Robert Windrem is a senior investigative producer.