Iran and al Qaeda's core leadership under Ayman al Zawahiri have established an "operational relationship" amid fears the terror group is planning a spectacular attack against the West.
There are concerns such an attack, possibly targeting Europe, would be in revenge for the killing of Osama bin Laden by the US last year.
Sky News' intelligence sources have said Iran has been supplying al Qaeda with training in the use of advanced explosives, "some funding and a safe haven" as part of a deal first worked out in 2009 which has now led to "operational capacity".
Although some Western intelligence agencies remain sceptical about an "alliance" between Iran and al Qaeda, the United States has become so concerned about the close relationship that late last year it issued a \$10m (£6.4m) reward for information leading to the whereabouts of a Syrian al Qaeda leader in Iran, Ezedin Abdel Aziz Khalil, better known as Yasin al Suri .
The reward offered for al Suri, 30, puts him on the same level as Mullah Omar, the leader of the Taliban in Afghanistan. Only al Zawahiri, who replaced bin Laden, has a higher price, \$25m (£16m), on his head.
According to Sky sources, Iran has reacted to the publication of al Suri's name by taking him into "protective custody".
"If someone got hold of him, he would have the most incredible amount of intelligence and so it makes sense to make sure that he is protected," said a source.
But al Suri has been swiftly replaced - a sign, Sky intelligence sources say, that the al Qaeda relationship with Iran is of great mutual importance.
The new al Qaeda leader in Iran, effectively the most important figure outside the core leadership based in the Federally Administered Tribal Areas of Pakistan, is Muhsin al Fadhli.
The al Qaeda leadership in Pakistan is worried it is losing its grip on the movement's "franchise".
Al Zawahiri is believed to be planning a "classic" al Qaeda attack, simultaneously on multiple locations, which would confirm the mantle he has assumed as the leader of the global jihad.
A source said: "Iran is the main route through which funding for the organisations is made, the main route for operatives to travel to Pakistan for training, and it is the only real way by which al Zawahiri can control and order a major attack."
The sources have no specific intelligence on what the al Qaeda target is, nor when it might be launched.
"We do know that an operation is under way. We assess that the most likely target is to be European. And the most obvious target in Europe for an attack that would attract a lot of attention would be the Olympic Games," a source said, stressing that this was only an "assessment" and not based on any specific intelligence.
The newly-appointed al Qaeda leader in Iran was accused of providing funding to its operations in Iraq. A Kuwaiti citizen, he fought in Chechnya and Afghanistan.
His deputy, Adel Radi Saker al Wahabi al Harbi, a Saudi, also served under al Suri and is on Saudi Arabia's "most wanted" list of alleged terrorists .
A secret intelligence memo, seen by Sky News, said: "Against the background of intensive co-operation over recent months between Iran and al Qaeda - with a view to conducting a joint attack against Western targets overseas... Iran has significantly stepped up its investment, maintenance and improvement of operational and intelligence ties with the al Qaeda leadership in Pakistan in recent months.
"Al Harbi (the al Qaeda number two in Iran) is considered an extremely dangerous field operative; he has fought in the Afghanistan and Pakistan theatres."
Iran's nuclear programme has been under covert attack for the last few years.
At least five nuclear scientists have been killed, or maimed, in hit-and-run shootings and bombings which Iran has blamed on Israel.
In addition, its efforts to develop a long-range missile and refine uranium to a weapons grade have been hit by 'accidents' and the Stuxnet computer virus, which temporarily crippled its uranium centrifuges.
This week Israel blamed Iran's client organisation, the Lebanese militant group Hizbollah, for two bomb attacks against Israeli targets - one in New Delhi wounded an Israeli diplomat.
Iran has denied any links to al Qaeda, and to the recent attacks on Israelis .
The intelligence sources said that Iran wanted to extend its global reach with al Qaeda "most likely to be used in revenge for any military strikes against Iran's nuclear capacities. Iran wants to be able to say 'We can hit you back'".
Israel, which would face an existential threat from a nuclear Iran, has been debating the merits and dangers of an attack on Iran.
It would face a bombardment of hundreds of thousands of rockets from Hizbollah in Lebanon and Gaza, and directly from Iran in retaliation for an attack on Tehran's nuclear programme, Israeli experts have warned.
"Iran wants to widen that response to a global threat against Western targets, probably as a deterrent to any strikes by the West against its nuclear facilities," a Sky source said.
"The danger is that Iran and al Qaeda may be keen to show this capacity ahead of any attacks on Iran - as a kind of warning."
Although Iran, as a Shia theocracy, would not be a natural bedfellow of the Sunni al Qaeda network, there is a precedent for Iranian support for Sunni terrorist groups.
Hamas, in Gaza, has received significant funds and weapons from Iran via Syria. And in Iraq allied troops were targeted by both Sunni and Shia militants with bombs developed with expertise from Iran and Tehran's proxy, the Hezbollah movement in Lebanon.