The fate of United Airlines Flight 93, the last of the four hijacked planes to go down in the United States on 11 September, holds no mystery for Lee Purbaugh. He saw what happened with his own eyes. He was the only person present in the field where, at 10.06am, the aircraft hit the ground.

"There was an incredibly loud rumbling sound and there it was, right there, right above my head – maybe 50ft up," says Purbaugh, who works at a scrapyard overlooking the crash site. "It was only a split second but it looked like it was moving in slow motion, like it took forever. I saw it rock from side to side then, suddenly, it dipped and dived, nose first, with a huge explosion, into the ground. I knew immediately that no one could possibly have survived."

Apart from, here and there, a finger, a toe or a tooth, all that remained of the 44 souls aboard, churned into the soil or hanging from the branches of nearby trees, were small pieces of tissue and bone. The plane was also pulverised, reduced to tiny fragments of metal. Wally Miller, the local coroner in what used to be a forgotten corner of rural Pennsylvania, was the man charged by law with collecting the human remains and establishing the causes of death. "I issued the death certificates," says Miller, who is also the local undertaker. "I put down 'murdered' for the 40 passengers and crew; 'suicide' for the four terrorists."

Download the new Independent Premium app Sharing the full story, not just the headlines

But Miller, who worked closely with the FBI during the 13 days that they investigated the crash site, admits that, in the end, he cannot prove what happened; he can only infer it. Neither he nor anybody else knows what exactly caused Flight 93 to go down and, as Miller puts it, "bring the world's troubles crashing down on our doorstep". Or, if there are people who do know, they are not telling.

The shortage of available facts did not prevent the creation of an instant legend – a legend that the US government and the US media were pleased to propagate, and that the American public have been eager, for the most part, to accept as fact. The legend goes like this: the passengers on the hijacked United flight, alerted on their mobile phones to the news of the other three hijacked planes, decide that if they are not going to save themselves at least they will do the patriotic thing and spare the lives of those who are the terrorists' intended targets; so they charge down the aisle, storm the cockpit, where a terrorist is at the controls, and, in the ensuing struggle, force the plane down.

President George Bush, Attorney General John Ashcroft, the head of the FBI Robert Mueller, and numerous other senior government officials who have saluted the "heroes" of Flight 93, have consistently, and repeatedly, advanced this version of events. So have the big national newspapers and all the big national television stations. The New York Times, normally a model of legalistic precision, published this extraordinarily woolly sentence on 22 September upon learning, from unnamed "official" sources, that the plane's cockpit voice-recorder had registered "a desperate and wild struggle" aboard. "And while it [the recorder] did not provide a clear or complete picture," The New York Times read, "it seemed certain that there was a chaotic confrontation that apparently led to the crash of the jet."

Vanity Fair magazine, going on little more information than was available to The New York Times, went ahead and published a highly detailed story on Flight 93, which, the magazine said, "may be remembered as one of the greatest tales of heroism ever told". Vanity Fair did recognise, though, that any suggestions as to what actually happened to force the plane down had to be, by necessity, "pure conjecture".

Two months later, Newsweek got hold of what it was told was a partial transcript of the voice-recorder and, upon that basis, narrated the story of "the Heroes of Flight 93" in even more vivid, drum-rolling, Hollywoodesque detail than Vanity Fair had done. The passengers were "citizen soldiers... who rose up, like their forefathers, to defy tyranny", intoned Newsweek. "In daring and dying, the passengers and crew of Flight 93 found victory for us all."

The transcript that Newsweek obtained did indicate that fighting had taken place aboard, curses had been uttered, prayers raised up both to the Muslim and the Christian god. But for all the drama of the story, Newsweek did not draw attention to the fact that, in truth, they were guessing as to how or why the plane had crashed; that they did not know whether the passengers had even made it into the cockpit; that they had no clue what happened during Flight 93's decisive, desperate last eight minutes.

Which is not to assert that the "hero" story is untrue, or even implausible. Maybe the legend does indeed correspond perfectly to the facts. And certainly, based on the records of telephone calls made from the plane, there is no disputing that a number of the passengers did indeed intend to carry out actions of great courage. But what those actions actually turned out to be is not known – or known only to a small group of people with a clear picture of what happened in the skies over Shanksville on the morning of 11 September, people in the US military who tracked the plane's last moments as well as people familiar with, but unwilling to reveal, the full contents of the material gleaned from the cockpit voice- recorder, which was retrieved in perfect working order after the crash.

Daily coronavirus briefing No hype, just the advice and analysis you need Enter your email address Continue Continue Please enter an email address Email address is invalid Fill out this field Email address is invalid Email already exists. Log in to update your newsletter preferences Register with your social account or click here to log in I would like to receive morning headlines Monday - Friday plus breaking news alerts by email Update newsletter preferences

The absence of official information has led to lively and often well-informed debate in the unofficial medium of the internet (see www.flight93crash.com.) But there are also a number of individuals in the aviation industry convinced that there do exist other plausible interpretations of what actually happened. Because there are, most certainly, a number of important unanswered questions – questions based on evidence, as well as on a manifest absence of candour on the part of the authorities – which the national US media, typically so sceptical and inquisitive, have shown a curious reluctance to ask.

The alternative theories, both of which have been denied by the US military and the FBI, are a) that Flight 93 was brought down by a US government plane; and b) that a bomb went off aboard (passengers had said in phone calls that one of the hijackers had what appeared to be a bomb strapped to him). If doubts remain despite the denials, if conspiracy theories flourish, it is in large part because of the authorities' failure to address head-on questions centring on the following four conundrums.

1. The wide displacement of the plane's debris, one explanation for which might be an explosion of some sort aboard prior to the crash. Letters – Flight 93 was carrying 7,500 pounds of mail to California – and other papers from the plane were found eight miles (13km) away from the scene of the crash. A sector of one engine weighing one ton was found 2,000 yards away. This was the single heaviest piece recovered from the crash, and the biggest, apart from a piece of fuselage the size of a dining-room table. The rest of the plane, consistent with an impact calculated to have occurred at 500mph, disintegrated into pieces no bigger than two inches long. Other remains of the plane were found two miles away near a town called Indian Lake. All of these facts, widely disseminated, were confirmed by the coroner Wally Miller.

2. The location of US Air Force jets, which might or might not have been close enough to fire a missile at the hijacked plane. Live news media reports on the morning of 11 September conflict with a number of official statements issued later. What the government acknowledges is that the first fighters with the mission to intercept took off at 8.52am; that another set of fighters took off from Andrews Air Force base near Washington at 9.35am – precisely the time that Flight 93 turned almost 180 degrees off course towards Washington and the hijacker pilot was heard by air-traffic controllers to say that there was "a bomb aboard". Flight 93, whose menacing trajectory was made known by the broadcast media almost immediately, did not go down for another 31 minutes. Apart from the logical conclusion that at least one Air Force F-16 – 125 miles away in Washington at 9.40am, meaning 10 minutes away from Flight 93 (or less if it flew at supersonic speed) – should have reached the fourth of the "flying bombs" well before 10.06am, there is this evidence from a federal flight controller published a few days later in a newspaper in New Hampshire: that an F-16 had been "in hot pursuit" of the hijacked United jet and "must have seen the whole thing". Also, there was one brief report on CBS television before the crash that two F-16 fighters were tailing Flight 93. Vice-President Dick Cheney acknowledged five days later that President Bush had authorised the Air Force pilots to shoot down hijacked commercial aircraft.

3. One telephone call from the doomed plane whose contents do not entirely tally with the hero legend and which is accordingly omitted in the Independence Day-type dramas favoured by the US media. The Associated Press news service reported on 11 September that eight minutes before the crash, a frantic male passenger called the 911 emergency number. He told the operator, named Glen Cramer, that he had locked himself inside one of the plane's toilets. Cramer told the AP, in a report that was widely broadcast on 11 September, that the passenger had spoken for one minute. "We're being hijacked, we're being hijacked!" the man screamed down his mobile phone. "We confirmed that with him several times," Cramer said, "and we asked him to repeat what he said. He was very distraught. He said he believed the plane was going down. He did hear some sort of an explosion and saw white smoke coming from the plane, but he didn't know where. And then we lost contact with him."

According to the information that has been made known, this was the last of the various phone calls made from the aeroplane. No more calls were received from the plane in the eight minutes that remained after the man in the toilet said that he had heard an explosion.

4. Eyewitness accounts of a "mystery plane" that flew low over the Flight 93 crash site shortly after impact. Lee Purbaugh is one of at least half a dozen named individuals who have reported seeing a second plane flying low and in erratic patterns, not much above treetop level, over the crash site within minutes of the United flight crashing. They describe the plane as a small, white jet with rear engines and no discernible markings. Purbaugh, who served three years in the US Navy, said he did not believe it was a military plane. If it indeed was not, one suggestion made in the internet discussion groups is that US Customs uses planes with these characteristics to interdict aerial drug shipments. Either way, the presence of the mystery jet remains a puzzle.

How has the US government and its various agencies responded to doubts raised by the above questions? In the following ways:

1. The paper debris eight miles away, the FBI says, was wafted away by a 10mph wind; the jet-engine part flew 2,000 yards on account of the savage force of the plane's impact with the ground. The FBI conclusion: "Nothing was found that was inconsistent with the plane going into the ground intact." Aviation experts I have contacted are very doubtful about this. One expert expresses astonishment at the notion that the letters and other papers would have remained airborne for almost one hour before falling to earth.

2. The Air Force jets were on their way but failed to make it on time, according to General Richard Myers, chairman of the joint chiefs of staff. Fighters did finally approach Flight 93, he acknowledges, "moments" before it crashed, but did not shoot it down. Which begs the question why they were unable to arrive sooner to intercept an aircraft that clearly had terrorists aboard and that was flying straight for Washington more than one hour after another United Airlines plane had crashed into the second World Trade Centre tower. The report in the New Hampshire newspaper, and the one on CBS, have not been explained, and the air-traffic controllers in Cleveland who tracked the last minutes of Flight 93 on radar have been forbidden by the authorities to speak publicly about what they saw on their screens.

3. Neither the FBI nor anyone else in authority has explained the reported 911 phone call from the plane toilet, even though it appears to be the last of the phone calls made from the plane and even though it conveys the far from insignificant claim that there was an explosion on board. The FBI has confiscated the tape of the conversation and the operator Glen Cramer has received orders not to speak to the media any more.

4. The explanation furnished by the FBI for the mystery plane, whose existence it initially denied, serves less to reassure than to reinforce suspicions that a cover-up of sorts is under way, that the government is manipulating the truth in a manner it considers to be palatable to the broader US public. The FBI has said, on the record, that the plane was a civilian business jet, a Falcon, that had been flying within 20 miles of Flight 93 and was asked by the authorities to descend from 37,000ft to 5,000ft to survey and transmit the co-ordinates of the crash site "for responding emergency crews". The reason, as numerous people have observed, why this seems so implausible is that, first, by 10.06am on 11 September, all non-military aircraft in US airspace had received loud and clear orders more than half an hour earlier to land at the nearest airport; second, such was the density of 911 phone calls from people on the ground, in the Shanksville area, as to the location of the crash site that aerial co-ordinates would have been completely unnecessary; and, third, with F-16s supposedly in the vicinity, it seems extraordinarily unlikely that, at a time of tremendous national uncertainty when no one knew for sure whether there might be any more hijacked aircraft still in the sky, the military would ask a civilian aircraft that just happened to be in the area for help.

Most suspicious of all, perhaps, has been the failure of the FBI or anybody else to identify the pilot or the passengers of the purported Falcon, and their own failure to come forward and identify themselves.

There was one other plane, a single-engine Piper, in the air as Flight 93 headed to its doom. The pilot, Bill Wright, said that he was three miles away and so close he could see the United markings on the plane. Suddenly he received orders to get away from the hijacked plane and to land immediately. "That's one of the first things that went through my mind when they told us to get as far away from it as fast as we could," Wright later told a Pittsburgh TV station, "that either they were expecting it to blow up or they were going to shoot it down – but that's pure speculation."

Everything is speculation – that is the problem with the story of Flight 93. And unless the US government reveals more of what it knows, provides a detailed account of the last 10 minutes in the life of Flight 93 and the 44 people who were aboard, there will not only be scope but sound reasons for the conspiracy theorists to continue to speculate as to what really happened in those last few minutes before the plane plunged into the earth; to cast doubts on the soft-focus legend that the traumatised American public has seized upon so gratefully.

Some conspiracy theorists will say that the plane was shot down by a missile, perhaps a heat-seeking missile that honed in on one of the plane's engines – a theory possibly substantiated by the 2,000yd flight of the 1,000lb engine part, but arguably refuted by consistent eye-witness accounts, including Lee Purbaugh's, that when last sighted the plane was not emitting smoke.

Others might say, as they have done about a TWA flight that fell to the sea in 1996 after taking off from New York, that the plane was a victim of electromagnetic interference. In the case of the TWA flight, the argument, put forward in a series of exhaustive articles written in the New York Review of Books by the Harvard academic Elaine Scarry, is that it happened accidentally. However, as Scarry's articles relate, documentation abounds showing that the Air Force and the Pentagon have conducted extensive research on "electronic warfare applications" with the possible capacity intentionally to disrupt the mechanisms of an aeroplane in such a way as to provoke, for example, an uncontrollable dive. Scarry also reports that US Customs aircraft are already equipped with such weaponry; as are some C-130 Air Force transport planes. The FBI has stated that, apart from the enigmatic Falcon business jet, there was a C-130 military cargo plane within 25 miles of the passenger jet when it crashed. According to the Scarry findings, in 1995 the Air Force installed "electronic suites" in at least 28 of its C-130s – capable, among other things, of emitting lethal jamming signals.

In decades to come, film-makers, future Oliver Stones, may come up with theories of their own, and the story of Flight 93 may come to acquire the morbid mystique of the Kennedy assassination.

None of which is to question the bravery of passengers such as Todd Beamer, who left behind a pregnant widow and two children aged two and three; or Tom Burnett, who had three small daughters and told his wife Deena over the phone, in the face of her anguished protests, that he and his fellow-passengers were "going to do something" because if not the terrorists were "going to run this plane into the ground". Evidently, as the Newsweek article relates, there was fighting of some kind, but as to whether the terrorists held off the passengers or the passengers seized control of the plane, and perhaps even made an attempt to fly it themselves (one passenger aboard was a qualified pilot of small planes), nobody knows – or is willing to admit that they know.

If evidence does exist further substantiating the hero narrative, it would be a surprise if the authorities had not released it. Bravery, though, there undoubtedly was. This we do know. As Lee Purbaugh says, and it would be churlish to disagree, "they were heroes on that plane". Such a consensus has been built around this view that the crash site at Shanksville – an anonymous-looking field save for the American flags that flutter all around, the crosses, the pictures of the dead passengers, the messages of goodwill and of good cheer ("Don't mess with the US!") – that it has become a place of pilgrimage, much as has happened with ground zero in New York but on a smaller scale, attracting some 150 visitors from all over the US every day. "In truth," said Wally Miller, who as coroner remains legally in charge of the site, "that field is a cemetery. It should be treated with due respect."

What does Miller think happened? Did he attach any credence to the stories doing the rounds, to those – including a number in Shanksville – who dissent from the official version of events? Miller, who has seen as much evidence as anybody at the scene of the crash, does not dismiss the dissidents out of hand. He keeps an open mind. "The order had been given to bring the airplane down," he said. "I do not rule anything out."