Robert Fisk: Khamenei is fighting for his own position as well as Ahmadinejad's

It was predictable, ruthless, alarming, intended to put the fear of God – yes, God indeed – into his enemies. "The time for competition is over," the Supreme Leader told us. "If street protests don't stop, there will be other consequences ... They will be held accountable for all the violence and blood and rioting ... There will be a reaction." It was a threat. Enough is enough. Or else.

Ayatollah Ali Khamenei was Thomas Cromwell yesterday, praising those he loathed with just enough directness for the recipient to know that a Supreme Leader's anger will embrace a senior cleric or two. When he expressed his admiration for Ali Akbar Rafsanjani's revolutionary credentials and added that "nobody has accused this gentleman of corruption" – who said they had? – you knew exactly what he meant. Think profits from pistachio nuts and the Tehran Metro. And when Khamenei said that "those who voted for these four candidates will have their rewards from God Almighty", you knew that most would not be rewarded with the president of their choice.

If it hadn't been so frightening, the Friday prayers sermon at Tehran University might have contained a perverse humour. "The Islamic establishment," Khamenei solemnly announced, "will never manipulate people's votes." If the margin between Ahmadinejad and Mousavi had been 100,000 or 200,000 votes, perhaps one might believe it, he explained. "But when the difference is 11 million votes, how can vote-rigging happen?" But that was just the point, wasn't it? That Ahmadinejad's awesome majority did indeed cast the whole shebang into doubt.

And our favourite divine went on. Of course the vote was fair – because the turnout (85 per cent?) was so high. This was religious democracy, not the corrupt Western version. "Some people wanted to show the election as a national defeat, but it was the highest turnout in the world." And of course, if the people did rashly take to the streets once more, "terrorists" – it's always good to hear Iran's religious elite use the West's favourite cliché – "might be hiding among the masses".

It was a sliding scale from there. Perhaps some of these people were working for foreign espionage services, for the Zionists, for that "most treacherous enemy", the British. Obama got short shrift, but his Cairo speech had clearly allowed us Brits to take over as Great Satan. The Supreme Leader didn't like all the pre-election television debates – one felt a twinge of warmth towards this eminent man of the cloth when he admitted he had nonetheless enjoyed them (we all did) – but where does this leave Mirhossein Mousavi and his allies and the million Iranians who marched through Tehran on Sunday? They were about to become enemies of the people, enemies of the revolution. It's one thing to say – as Mousavi's loyalists have done consistently – that their protest is only against a fraudulent vote and the awful Ahmadinejad, not against the Supreme Leader. But now this Islamic Thomas Becket has set himself up alongside Ahmadinejad, the demonstrators have found themselves confronting the power of the Islamic Republic, a pretty unsatisfactory state of affairs.

But the Supreme Leader is not a stupid man. So why did he glue himself to Ahmadinejad? Could it be he is worried about another very powerful clergyman who lives in the golden-domed city of Qom, a certain Ayatollah Yazdi who has long feted and praised the aforesaid Mahmoud Ahmadinejad? And is it possible – it is, by the way – that Ayatollah Yazdi would very much like to be the next Supreme Leader?

Good reason then for Khamenei to stand by the President who insisted a halo shone around his head when he addressed the UN.

Because the fundamental conflict in Iran is being fought not on the streets of Tehran – a mere tragic, brutal sideshow that could soon become a bloodbath – but beneath the cupolas and minarets and pale blue tiles of the mosques of Qom.