With a showdown looming between rival factions in Iran Thursday, the country's Supreme Leader, Ayatollah Ali Khamenei, looks to be in a precarious situation.

If he orders his military to take aggressive action against the expected massive protest, the man who has held this supreme position for 20 years will lose popular credibility. If he tells his forces to stand down, he will jeopardize the faction he has openly endorsed – the one of Mahmoud Ahmadinejad and the Revolutionary Guard.

It wasn't supposed to be this way.

When the late ayatollah Ruhollah Khomeini defined the position of Supreme Leader, he saw it as the Islamic Republic's supreme power, above the political fray. During the past two decades, however, Supreme Leader Khamenei has come down from the heights and joined the political battle a number of times. The most recent was his open support for Mr. Ahmadinejad in the election and welcoming of Mr. Ahmadinejad as the winner Friday night.

Having sought to use his supreme power to influence the outcome, he has lost his supremacy in many people's eyes.

So why did he do it? Why get down and dirty when he had so much power?

“He has always needed to establish his authority,” says David Menashri, chairman of modern Iranian studies at Tel Aviv University. “He may have the title but, even after 20 years, he still doesn't have the authority.”

“He knows that many people in the establishment think he's not up to the job.”

And it's those people in the establishment – they include Mir-Hossein Mousavi, Mr. Ahmadinejad's rival for the presidency, and, more importantly, former president Ali Akbar Hashemi Rafsanjani – who are trying to reduce the influence of this Supreme Leader even more.

“If Khamenei loses any more ground,” says Saeed Rahnema, an Iranian-born political scientist at York University in Toronto, “both he and the military-security establishment will suffer a near irreparable blow.”

Ayatollah Khamenei got the job of Supreme Leader by being in the right place at the right time.

When the iconic ayatollah Khomeini died in 1989, there was a political battle to see who should rule in his wake. With the help of Mr. Rafsanjani, then chairman of the Majlis, Mr. Khamenei, then in the eighth year of his presidency, was chosen as a compromise. It was a big surprise, since the 49-year-old figurehead president didn't have the credentials of a religious scholar.

True, he had translated the works of the radical Islamist Sayed Qutb into Persian, had lost the use of his right arm in an assassination attempt, and wears the black turban of a direct descendent of the Prophet Mohammed, But Ayatollah Khamenei lacked the religious scholar's pedigree.

“He was only half an ayatollah,” Prof. Menashri said. “Then, overnight, he became a grand ayatollah. People had trouble accepting it. It was all politics, not religion.”

For a time, the new Supreme Leader and Mr. Rafsanjani helped each other.

Mr. Rafsanjani got support becoming president that year, and help in eliminating the position of prime minister (held by Mr. Mousavi) to better concentrate power in the hands of the president.

Mr. Rafsanjani also “understood that in order to push his [economic reform] agenda forward he had to form a tactical alliance with the … Leader,” writes Ghoncheh Tazmini in Khatami's Iran . In exchange for all that, Ms. Tazmini says, “Khamenei's position was reinforced with the addition of the expression ‘absolute' into his constitutional title.” Henceforth, he was the Supreme Leader.

Lacking a political base, Ayatollah Khamenei set about from the beginning courting the country's powerful Revolutionary Guard. Coming off an eight-year war with Iraq, the numerous guardsmen were in need of jobs and the Ayatollah saw that they got them; not just in the military, but in most walks of economic life.

And this is when the battle began between Ayatollah Khamenei and then-president Rafsanjani, Prof. Menashri says. “Rafsanjani had always thought he could marginalize Khamenei,” he said. “He hadn't counted on Khamenei falling in love with power.”

During Mr. Rafsanjani's second term, from 1993-97, writes Ms. Tazmini, “cracks began to show in the system.”

The Supreme Leader joined forces with the Majlis Speaker, Ali Akbar Nateq-Nouri, who opposed the president's reforms, Ms. Tazmini says, and “Rafsanjani was rendered politically impotent.”

Constitutionally barred from seeking a third term, Mr. Rafsanjani put forward Mohammad Khatami, a hitherto obscure culture minister, as presidential candidate in 1997, to take the reform program forward.

Riding a wave of popular support from women and youth – not unlike what was seen backing Mr. Mousavi in the most recent election – Mr. Khatami came to office with a strong mandate. He, too, set about making reforms – for a freer press, greater rights, etc. – only to see many of them undone by the Supreme Leader and the ultraconservative faction he favoured.

In 2000, writes Ms. Tazmini, after the conservative judiciary shut down 18 of the 20 pro-reform publications that had started up under president Khatami, the Supreme Leader himself waded in to prevent parliamentarians from trying to overturn the court's restrictive ruling on press freedom.

Mr. Rafsanjani tried to take back the presidency, running to succeed Mr. Khatami in 2005, only to run into the Supreme Leader's candidate, the populist mayor of Tehran, Mr. Ahmadinejad, to whom he lost in a runoff.

“The animosity between these guys goes all the way back to these events,” Prof. Menashri said.

And now, once again, the Supreme Leader finds himself in a battle of wills with Mr. Rafsanjani.

“Khamenei still has lots of cards to play,” Prof. Menashri said, “but most of them involve the threat or use of force against the people.

“He can't pretend to be above it all; it's too late for that,” he said.

“But, in the name of the survival of the Islamic Republic, he might call for unity between the factions – a kind of national-unity government, with some kind of division of authority.”

It's either that, or some kind of negotiated retreat, Prof. Menashri said.

“There are people who say Rafsanjani is in Qom right now, negotiating some kind of deal,” he said. The Assembly of Experts has the power to call for Ayatollah Khamenei's resignation, and Mr. Rafsanjani is its elected chairman.

The problem, says Mr. Rahnema, is that the Supreme Leader may not be making the calls any more.

“The Revolutionary Guards have a lot to lose if Ahmadinejad and Khamenei fall,” he explained. “They may be pushing the Leader to take precipitous action.”

It was the support for the Guards' economic and other opportunities that gave Ayatollah Khamenei a powerful political base. But, Mr. Rahnema says, “he may have created a monster he cannot control.”