She stands in the empty room, a deplorable, terrible, pitiful sight. Is it Margaret Hassan? Her family believe so, even though she is blindfolded. I'm not sure if videos like this should ever be seen – or perhaps the word is endured – but they are part of the dark history of Iraq, and staff of the Arab Al Jazeera satellite channel have grown used to watching some truly atrocious acts on their screens.

The "execution" – the cold-blooded, appalling murder of Margaret Hassan, the Care worker who was a friend as well as a contact of mine – is among the least terrible of the scenes that lie in the satellite channel's archives.

Kidnapped by men in police uniforms, it is now November, 2004, and Margaret has already made her last appeal. Viewers saw her begging Tony Blair to help her, to withdraw British troops from southern Iraq. "I beg of you to help me," she says in a voice of great distress. But there was then another tape which Al Jazeera refused to show, in which Margaret was coerced into claiming that she gave information to American officers at Baghdad airport. A man's voice prompts her to keep to a text. "I admit that we worked with the occupation forces ..." she says. It is untrue, of course. Margaret was against the whole Anglo-American invasion. She would never have spied on Iraqis.

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Then comes the last tape. She is standing in that bare room in a white blouse, a blindfold over her face, her head slightly bowed and a man approaches her from behind holding a pistol. He points it at her head and places what appears to be an apple over the muzzle – a primitive form of silencer? And then squeezes the trigger. There is a click, an apparent misfire, and the man retreats to the right of the screen and then reappears. Margaret Hassan doesn't move although she must have heard the click. The man is wearing a grubby grey and black checked shirt and ill-fitting, baggy trousers, a scarf concealing his face.

This time the gun fires and the woman utters a tiny sound, a kind of cry, almost a squeal of shock, and falls backwards onto the floor. The camera lingers on her. She has fallen onto a plastic sheet. And she just lies there. There is no visible blood, nor wound. It is over. Should such terrible things be seen? Margaret's immensely brave Iraqi husband told me I had his permission to watch this, but still I feel guilty. I think it was only here, watching her death on a screen next to Al Jazeera's studios more than three years later, that I realized Margaret Hassan was dead.

It was Margaret who took leukaemia medicines donated by readers of The Independent to the child cancer victims of Iraq back in 1998 after we discovered that hundreds of infants were dying in those areas where Western forces used depleted uranium munitions in the 1991 Gulf War. She was a proverbial tower of strength, and it was she – and she alone – who managed to persuade Saddam Hussein's bureaucrats to let us bring the medicine into Iraq. The United Nations sanctions authorities had been our first hurdle, Saddam Hussein our second. It is all history. Like Margaret, all the children died.

"We've trained ourselves not to go to the maximum in our feelings when we see terrible things like this," Ayman Gaballah, Al Jazeera's deputy chief editor, says bleakly. And I can see why. There are other tapes, other outrages too terrible to show. George Bush wanted to bomb the station's headquarters in Doha but staff have shown great sensitivity with what they show the world from Iraq. There is no proof that any of Al Jazeera's reporters was ever tipped off about anti-American attacks before they happened – in Iraq, I investigated these claims in 2003 and 2004 – but plenty of proof that some things are too awful to see.

On one tape, a half-naked man is held to the floor while another produces a small butcher's knife and slowly carves his way through the victim's throat, the poor man's shriek of pain dying in froths of blood until his head is eventually torn from his body.

Another tape shows 18 Iraqi policemen held captive against a demand for the release of Iraqi women prisoners. They are aged between 17 and 40 and stare at the camera hopelessly.

Al Jazeera aired the pictures and the written demands but then cut the next scene. It shows the 18 men trussed up and blindfolded in front of a ditch. A hooded man then fires into the back of one of their heads and – along with other men off-camera – goes from one body to the next, firing again and again. Some of the victims are still alive, their legs kicking and the hooded man goes to each one and fires again into their heads. Then, in the background, a bearded youth approaches the camera, holding an Islamic flag. He is singing.

For some in the Al Jazeera studios these archives are intensely personal. "I trained Ali Khatib – he was a great reporter," I am told. "The war was almost declared at an end in Iraq and he went out with our cameraman to cover some story and, while he's approaching an American checkpoint, you can hear an American soldier on the tape say 'Stop – you have to go back'. And then the soldier just shot at them and killed both of them. Ali had got married two weeks earlier."

For some, the videotapes will always be too much. When I met Margaret's husband Tahseen in his Baghdad home after her murder, he was a picture of courage and mourning. There were terrible times. "I would come home and sit here and weep," he told me then. "I would sit here sometimes and go out of my mind crying and sobbing. I don't think insurgents did this. I don't think Iraqi people did this ... I couldn't see the video that was released – not because she's my wife, but because I can't bear to see anyone assassinated."

So who did murder Margaret Hassan? On the video of her apparent execution, there are no Islamic banners, no Muslim chants, no claim of responsibility, just the killer and the fatal shot. After her kidnap, Margaret – who once worked as an English-language newsreader on Saddam's government television station in Baghdad – even found support among the anti-American insurgents; they issued a joint appeal for her release. Even Abu Musab Zarqawi, the al-Qa'ida leader in Iraq who was later killed by the Americans, joined in the appeal. Margaret had worked in Palestinian camps in the 1960s and fought tirelessly for those thousands of Iraqis under her care in Iraq. If her husband's suspicions were correct, then whose "foreign" hand took her away?

The tape leaves no clue. In Al Jazeera's archives, it is difficult to escape this repository of death. The Americans fired a cruise missile at Al Jazeera's Kabul office in 2001 after it had forwarded Osama bin Laden's tapes to Doha. Then an American aircraft fired a missile at the station's Baghdad office in 2003. That time, the Americans killed the bureau chief, Tareq Ayoub. His jacket and his last notes are today on the wall of Al Jazeera's Doha head office. His staff had – for their own protection – earlier given the map coordinates of their Baghdad office to the US State Department. Reporters asked Tony Blair – on a post-prime-ministerial tour of the Doha offices – if Bush had really planned to bomb them. "Blair said something about 'the need to move on'" one of them told me. "So we knew it was true."

If Al Jazeera's staff have paid a terrible price for their reporting and have been the witnesses to some of the ghastlier acts in Iraq, they appear to have the ferocious support of the Emir of Qatar, Sheikh Hamad bin Khalifa al-Thani, who spends his millions funding the loss-making station.

Stories abound of the day that George Tenet – then America's CIA chief – turned up in Qatar to give the Emir a dressing down for Al Jazeera's reporting. There was a stiff row between the two men before the Emir walked out.

In Washington, he was invited to meet Vice-President Dick Cheney, only to find that Mr Cheney had a thick file on his desk when he walked in. It was Mr Cheney's list of complaints against Al Jazeera. The Emir told him he would not discuss it. "Then that is the end of our meeting," Mr Cheney announced. "It is," the Emir apparently replied. And walked out. The "meeting" had lasted 30 seconds.

But those are the high points, the drama of Al Jazeera. The dark moments are on those terrible tapes. I asked some of the reporters how humans could commit such atrocities. None of them knew.

One suggested that 11 years of UN-imposed sanctions had somehow changed the mentality of Iraqis. And I do recall, back in 1998 – when Saddam still ruled Baghdad – an NGO official tried to explain to me what was happening to Iraqis. The Americans and British "want us to rebel against Saddam," the official said. "They think we will be so broken, so shattered by this suffering that we will do anything – even give our own lives – to get rid of Saddam. The uprising against the Baath party failed in 1991 so now they are using cruder methods. But they are wrong. These people have been reduced to penury. They live in shit. And when you have no money and no food, you don't worry about democracy or who your leaders are."

That official was Margaret Hassan.