Three years on, the sweet factory has a new roof and Amin's leg has mended. Fadil Reheima, also on duty that night, squats nodding and smiling beside him. Fadil, 32, cannot tell me what he remembers, however, because he has been deaf and dumb since the attack.

The missiles that flattened al-Shifa were launched from a submarine in the Red Sea two weeks after 224 people were killed by bomb blasts at the American embassies in Nairobi and Dar es Salaam. Al-Shifa was part-owned by Osama bin Laden, the main suspect for the attacks, and was producing nerve gas, Bill Clinton said. Against the advice of appalled British diplomats, Tony Blair backed him to the hilt.

But by the time the first TV crews arrived in protective clothing, it was already clear that something was wrong. The fallout of aspirins, carpeting the sandy ground all around, gave it away. So did the fact, overlooked by American intelligence, that the factory was privately owned, though part-financed, by a Kenya-based development bank.

"The evidence was not conclusive and was not enough to justify an act of war," concedes Donald Petterson, former American ambassador to Sudan. With a £35m compensation claim working its way through the American courts, that is as much as any official will say on the record. The evidence was supposed to consist of incriminating soil samples; they have never been produced. Sudan's proposal that the UN should investigate was vetoed by America. And Washington is currently trying to fight the case by pleading sovereign immunity. But shortly after filing his suit, the factory's owner, Salah Idris, had his American bank accounts quietly unfrozen.

Idris probably did have dealings with Bin Laden. As one of Sudan's richest businessmen, it would have been difficult not to. Bin Laden was based in Khartoum for five years, building bridges, roads and farms (and, of course, his al-Qaida terrorist group). But he was ushered out of Sudan a good two years before al-Shifa was flattened with such brilliant precision.

Dr Idris Eltayeb, one of Sudan's handful of pharmacologists and chairman of al-Shifa's board, is still impressed by the mathematics of it. "To be able to pinpoint this little factory from thousands of miles away - it's incredible," he says, walking around the mounds of rubble, left lying as it fell, littered with thousands of vials of livestock antibiotic and strips of malaria tablets.

But if Eltayeb is alive to the absurdity of American hi-tech pitted against "a simple factory in one of the poorest countries in the third world", he can also count the cost. Al-Shifa was one of only three medium-sized pharmaceutical factories in Sudan, and the only one producing TB drugs - for more than 100,000 patients, at about £1 a month. Costlier imported versions are not an option for most of them - or for their husbands, wives and children, who will have been infected since. Al-Shifa was also the only factory making veterinary drugs in this vast, mostly pastoralist, country. Its speciality was drugs to kill the parasites which pass from herds to herders, one of Sudan's principal causes of infant mortality. Since the bombing, "people have gone back to doing without," says Eltayeb, with a shrug.

Nobody was killed outright. "But this was just as much an act of terrorism as at the twin towers - the only difference is we know who did it," Eltayeb says. "I feel very sad about the loss of life there, but in terms of numbers, and the relative cost to a poor country, this was worse."

Still worse than the cost to Sudan's fragile medical services was the political cost to a country struggling to emerge from totalitarian military dictatorship, ruinous Islamism and long-running civil war. Ten years after President Omar al-Bashir seized power, a defiant policy of offering refuge to Muslim brothers had turned Sudan into a pariah state. Ethiopia, Eritrea, Kenya and Uganda were backing Christian rebels in the south. The economy was in ruins. And so Khartoum was being forced to open up. The terrorists - famously, Bin Laden and Carlos the Jackal - had been kicked out. The government was talking to its neighbours. Then al-Shifa was bombed, and overnight Khartoum was plunged into the nightmare of impotent extremism it had been trying to escape.

Sudan is still struggling to purge itself of the diehards. It has more or less convinced its neighbours to stop backing the rebels, opposition parties have been restored, and oil contracts are now awarded on the basis of tender rather than religious fervour. At the same time, arbitrary police powers have been beefed up, trade unions and political rallies remain effectively banned, floggings and amputations are routine, and so farcical were last year's presidential elections that all except stooge opposition parties boycotted them.

At the very best, these contradictions are embarrassing, but further missile strikes - Sudan remains on America's hitlist of states sponsoring terrorism - will not coax it along any quicker.

"The way to eradicate international terrorism is not to throw cruise missiles around. It is to get rid of ruthless dictatorship and promote democracy," says Ghazi Suleiman, a human rights lawyer who has been arrested by his own government "countless times", but who is also, not coincidentally, suing America on behalf of Idris. Bad politics, not bad religion, produces terrorism, says Suleiman. And it is this that America must attack. "Bush tells us he will smoke Bin Laden out of his cave. But truly the caves he is talking of do not exist only in Afghanistan. These caves are all over Africa and the developing world."

In Khartoum's mosques, Bin Laden and America are keeping the imams busy. "America is reaping what it has sown. Hiroshima, Nagasaki, Korea, Vietnam, Iraq, Palestine: Muslims must fight this jihad together," Sheikh Mansoor Hussein told the faithful at last Friday's prayers. America's TV evangelists have been invoking a similar kind of crusade to free Sudan's Christians for years. After prayers, the sheikh claimed that 4,000 Jews did not show up for work at the World Trade Centre on September 11. "We know who is responsible," he said.

But outside El Sheid mosque there are no signs that the faithful are answering the call. Unlike in predominantly Christian Nairobi or Kampala, pictures of Bin Laden are nowhere to be seen. Musa al-Hadi offered the exception - on the cover of the Arabic Newsweek he was hawking in the traffic. "Business is so-so," he says, "maybe a bit better than usual, not much." Nobody is crowing over America's misfortune, says leading journalist Khatim Mahadi, because, unlike westerners, Africans are used to distinguishing between bad governments and innocent citizens. "We have more experience of suffering than you," he says. "We know what brutality is."

Since the terror attacks, Washington has praised Khartoum for rounding up 30 suspects, providing intelligence on Bin Laden, and offering its airbases for strikes against Afghanistan. But, strangely, Khartoum denies doing any such things. "We haven't offered any airstrips and we just hope America isn't going to act without evidence this time," says information minister Mahdi Ibrahim Mohamed.

This may only show that old habits die hard. America finally agreed to a lifting of UN sanctions against Sudan on Friday. But Mahadi had great trouble getting the story past the government censor. "He thought we weren't supposed to mention America, whatever it was about," Mahadi says. Now Sudan wants America to end its own, much more serious, trade sanctions - from which only gum arabic, a crucial ingredient of Coca Cola, is exempt.

No one suffered from America's last war on terrorism more than Wol Bol, 32, another of the sweet factory's nightwatchmen. Almost his entire body was burned in the blast; his broken legs have left him crippled; his hair and finger-nails have not grown back. Wol and his wife Teresa, 28, are from the Christian Dinka tribe. They fled to Khartoum when their village was razed right at the beginning of the civil war.

After the bombing, Wol was unconscious for almost three months. Only when he was moved to the holy martyrs' ward, for government soldiers wounded in the south, did he start to improve. Now he is being treated in Cairo at the hospital's expense, says Teresa, "getting bits of his body cut off to stick on to other bits". Teresa badly wants to return to the south. Failing that, she would like to move her husband to America, she says, "because there is no war there".