To the average Heathrow traveller, it must have looked like just one of those inexplicable minor commotions that occur sometimes in the world's busiest airports. An El Al flight was standing on the runway, with some passengers still inside. Telephone calls were being made. Messages were passed to and fro. After two hours, the plane took off. No visible drama.

We now know that the story could have turned out very differently. Inside the plane was a senior Israeli army officer, Doron Almog, veteran of some of the most celebrated military operations in the troubled history of the Middle East. There were also armed Israeli sharpshooters.

Outside were officers of the Metropolitan Police, acting reluctantly on an arrest warrant served by a judge at the request of lawyers who wanted to launch a private prosecution against the general.

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The question that can never be answered is what would have happened if the police had marched on to the plane to seize the general and haul him before the courts. Possibly, he would have come quietly, and a lot of lawyers would have been kept very busy as the courts weighed what to do next.

A much more sinister possibility is that the Israeli agents on board would have refused to let the general be arrested without putting up resistance. At best, that would have meant an ugly stand off followed by a major diplomatic row. At worst, it could have led to dead bodies aboard the plane.

But now, the police and the Government face some awkward questions, of which the most interesting is who warned the Israelis that there was trouble brewing at Heathrow?

Maj-Gen Almog had planned to visit the UK in September 2005 to pay various social and charitable calls on Jewish communities in Solihull, the West Midlands, and Manchester. As his plane touched down at Heathrow, a call from the Israeli embassy in London warned him that police were waiting to arrest him. The general and his wife refused to leave the plane. Two tense hours elapsed, while Det-Supt John MacBrayne, a senior counter-terrorism officer in charge of the operation, agonised over what to do.

One of his problems, according to documents that have come to light, which were passed to the Independent Police Complaints Commission, was that he was unsure of the legal position. He contacted Scotland Yard for advice on whether he had the authority to order his men aboard the El Al aircraft, when it was clear the airline was not going to give consent. According to the official log: "He was informed that police did indeed board aircraft routinely but it was not clear if this could be done without the consent of the carrier. It was confirmed that El Al were refusing voluntary access to the plane and Det-Supt MacBrayne could not get confirmation that he had a legal right to do so."

But the log also shows that Supt MacBrayne had a problem. As an experienced anti-terrorist officer he knew that El Al aircraft are the most heavily guarded vehicles in the world. The seats on its aircraft are never filled only by ordinary fare-paying passengers. There are always at least a couple of men who are highly trained, heavily armed "air marshals". With a famous major-general on board, there might have been four or five air marshals. These are not people that any police officer would want to mess with.

"DSU MacBrayne took the considered opinion that, as access to the plane would not be consensual, there existed a real threat of an armed confrontation," the log recorded.

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Having consulted Commander John McDowall, deputy national co-ordinator of terrorist investigations, the Superintendent decided to allow the plane to go on its way with his quarry still aboard.

The Independent Police Complaints Commission has vindicated the police who conducted the operation. But that leaves two big questions unanswered – who tipped off the Israelis, and why did the Met seem to think they did not have the power to board an aircraft on British soil?

The legal position, which seemed to have the Met stumped, was actually straightforward, according to several legal experts who were asked their opinion yesterday. A foreign aircraft is not sovereign territory, and while it is on British soil it is subject to British laws. Even the threat of a shoot-out should not have prevented the police from enforcing the law, Kate Maynard, of the solicitors' firm, Hickman Rose insisted. "Who knows what might have happened?" she said. "It need not have been an armed stand off. They could have stopped the plane from taking off, and brought in negotiators from the Foreign Office. Can you allow people from other countries to put the police in a situation where they can't enforce British law?"

The Anti-Terrorist Branch had been reluctant all along to take any action against the general. They acted only under pressure from Hickman Rose, who represents Palestinian clients, including the Palestinian Centre for Human Rights. The lawyers themselves are not Palestinian. Several are Jews, and of those, Daniel Machover is an Israeli citizen – facts that have played big in the Israeli media. Mr Machover has been accused by Israel's most popular newspaper, Yedioth Ahronoth, of committing "a travesty masquerading as righteousness, exonerating terror-masters from blame but painting those who fight mass murderers as villains".

One of the firm's clients is Abdul Matar, the former inhabitant of one of 59 homes in a Palestinian camp that were bulldozed by the Israelis in 2002 in retaliation for attacks on Israeli soldiers. Another is Ra-ed Mattar, whose wife and daughter were killed when the Israelis dropped a powerful bomb in a crowded part of Gaza in July 2002, killing Sheikh Saleh Shehadeh, a leading Palestinian militant. The bomb killed 14 others including nine children.

Under pressure from the lawyers, the Anti-Terrorist Squad agreed that they would detain the general if he set foot on British soil, and would consider serving him with a warrant, but it would be up to the solicitors to bring a private prosecution. They intended to rely on a 50-year-old act of Parliament, the Geneva Conventions Act, which enshrined the Geneva Convention in British law. No one has ever been prosecuted under that Act.

The Anti-Terrorist Squad was also feeling discreet pressure from the Government to leave the general alone. Supt MacBrayne had had a note from a minister at the Foreign Office – whose name is not revealed in the log – who claimed that there was "little or no evidence" on which to launch a prosecution. Mr MacBrayne felt obliged to contact the Foreign Office and point out this was not true. Hickman Rose had in fact produced evidence that satisfied a magistrate that there was a case for the general to answer at least in relation to the bulldozing of those 59 homes. It also believed it could substantiate three other criminal charges against him.

He is not the only senior Israeli in its sights. Just over a year ago, the Israeli army's former chief of staff, Moshe Ya'alon, was arrested in New Zealand, after Hickman Rose took out a private case against him over the assassination of Sheikh Shehadeh. The case was ruled out by New Zealand's attorney general.

When Tony Blair met Israel's Internal Security Minister, Avi Dichter, last August, in his new role as Middle East peace envoy, he was dumbfounded to learn that Mr Dichter dare not visit the UK, where he too would risk being arrested over the Shehadeh killing. Two others, the Chief of Staff Dan Halutz and a former commander of the Gaza division, Aviv Kochavi, are also keeping away from the UK, for the same reason.

Doron Almog has been a well-known public figure in Israel since 1993, when he was appointed commander of the occupation forces in the Gaza Strip. By then, he had already had a colourful military career. When he was 22, he led a paratrooper unit into action in the Yom Kippur War.

Three years later, in July 1976, he was one of the Israeli commandos who descended suddenly on Entebbe airport, in Uganda, where over 100 crew and passengers of an airbus were being held hostage by Palestinian hijackers. When the shooting stopped, all six hijackers, one commando, three hostages and 45 Ugandan soldiers were dead.

In December 1993, Mr Almog stunned Israel by sensationally announcing that he had met members of Hamas, the militant organisation that is now the elected government of Gaza. Even now, most governments in the world, including the UK, refuse to recognise the Hamas administration, because Hamas will not recognise the state of Israel.

Mr Almog made two seemingly contradictory claims: first that he knew Hamas was preparing to send suicide bombers against Israel, secondly that there was a moderate faction within Hamas with whom Israel could do business. He claimed its hostility to the PLO exceeded its hostility to Israel. Hamas claimed the meeting had never taken place.

Mr Almog has attracted international attention for his role as head of Israel's Southern Command from 2000 to mid 2003, when he was in charge of operations in Gaza, and presided over the demolition of an estimated 1,100 Palestinian homes.

Before his planned UK visit, in September 2005, the police had also been warned that arresting a prominent Israeli might trigger a reaction among British Jews. Their original plan had been to detain General Almog in Solihull, where he was scheduled to speak in the synagogue, but they were warned that that would be inflammatory.

To lessen the tension, they decided a uniformed officer would be the one to make the arrest at Heathrow. Even so, the advice from the Met's National Community Tensions Team was that "this matter was of national significance to the Jewish community... any police action could significantly impact on community confidence in the police."

After the botched arrest, Mr MacBrayne checked with the West Midlands police and the Jewish community and reported that "there had been no local Jewish community issues."

But the Israeli government was enraged that one of its military heroes should be made so unwelcome in the UK, though it was mollified by an apology from the Foreign Secretary, Jack Straw. That apology has attracted derision from lawyers.

"He apologised for a judicial process," Mr Maynard said. "This case was not a stunt; it was an effort to bring Almog to justice in a place where he would have a fair trial, because he has complete immunity in Israel. To have it thwarted, and then to have an apology, is incredible."

That being the British Government's attitude, perhaps it is not surprising that somebody, somewhere, took it upon themselves to warn the Israelis that it would save both countries a serious embarrassment if Maj-Gen Almog did not alight from that plane.