On the border between Thailand and Cambodia, a mighty battle is taking place – and the outcome will determine whether millions of people live or die.

If the right side falters and fails, the long list of the dead will consist overwhelmingly of children and pregnant women. But this fight is passing virtually unnoticed in the outside world. Why? Because the lives at stake are – initially, at least – "only" "those of Asians and black Africans.

The war is against a tiny parasite that is suddenly – and rapidly – stripping away our ability to treat one of the deadliest diseases known to man. If the war fails, we will be left defenceless before it.

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Malaria is already the biggest killer in the world after Aids and tuberculosis. It infects 250 million people a year – the vast majority in Africa – and kills 1.5 million of them. In the Central African Republic last year, I met a woman the same age as me, 30, who was stalking her village, howling and ripping at her hair. She stopped long enough to tell me she had given birth to four children, and three had died spasming and shrieking of malaria. Now her youngest baby had all the symptoms, and she couldn't bear it. "Why is this happening? Why?" she kept yelling, to herself, to the sky, to no one.

It is caused by a parasite carried in the saliva of female mosquitoes. Once they inject it into your blood with a bite, the parasite heads for your liver and slows your blood flow. Within a few days, your organs fail. This happens to an equivalent of seven jumbo jets full of children every day.

The great Polish war correspondent Ryszard Kapuscinski described what it feels like. "The first signal of an imminent malaria attack is a feeling of anxiety, which comes on suddenly and for no clear reason. Something has happened to you, something bad," he wrote. Then comes "the dullness, the weakness, the heaviness ... Everything is irritating. First and foremost the light; you hate the light. But you don't have a lot of time for these loathings. For the attack arrives quickly. It is a sudden, violent onset of cold. Someone has taken you naked and thrown you into the icy highlands of Greenland."

At this point, "You begin to tremble, quake, thrash about. You immediately recognise, however, this is not a trembling you are familiar with; these tremors and convulsions tossing you around are of a kind that at any moment now will tear you to shreds." He said it is like being imprisoned "inside a mountain of ice" and slowly crushed.

Up until this year, the world was making remarkable progress in whittling down this disease. Since the year 2000, seven of the worst afflicted countries in sub-Saharan Africa have slashed malaria deaths by 50 per cent. It has a great knock-on effect too: for every £1 spent on malaria prevention, Africa gains £12 in economic growth, because people can work instead of lying sick and dying. It was a sign that aid, matched by good African government, can produce inspirational results.

But then something began to change – at first imperceptibly – in the forgotten forests of Western Cambodia, where the Khmer Rouge held their last stand-off. The drug that is most effective at treating malaria is called artemisinin: it shocks the parasite out of your system and saves your life. But in south-east Asia, horrified doctors have discovered that the malaria parasite is becoming resistant to it. In a Darwinian arms race, it has begun to evolve a way to beat the treatment. It is taking twice as long to work – and soon it will have defeated the medicine altogether.

We have been here before. In exactly the same place in the 1960s, the malaria parasite outraced the best available treatment of its day, choloroquine, and rendered it useless. The new super-parasite then spread rapidly to Africa. Across the map of the world, the ability to treat malaria was blacked out, region by region. Nick Day, Professor of Tropical Medicine at the Mahidol Oxford Clinical Research Unit, working on the ground, says: "It caused millions of deaths. If we let it happen again, we will face a major public health catastrophe."

It took 20 years for another medicine as effective as choloroquine to be developed. Millions of Africans died waiting. If we lose artemisinin, we will face another deadly interlude – and given that pharmaceutical companies are doing virtually no work on diseases that afflict poor countries because there is no profit in it, it could last indefinitely. Professor Day says: "There are no new malaria drugs coming down the pipeline. There is nothing to replace them for the foreseeable future." The broken mother I saw in Central Africa would then be one of many, many more.

Nobody knows why Cambodia's malaria parasites are such buffed-up hyper-Darwinian winners – the Mr Universe of the parasite world. They have in the past rendered other treatments like SP and DDT far less effective by evolving resistance to them too. Some scientists think it is because the treatments have been used there longer than anywhere else, giving their parasites a head-start. But it is not inevitable that this super-malaria will spread to Africa and cull millions. The scientists on the ground say we can contain them in Cambodia and prevent a disaster – if we act fast.

The scientists' plan is simple. It is to first of all massively suppress the spread of malaria in this area by a vast distribution of insecticide-treated mosquito nets, which have been shown to cut transmission by 80 per cent. Then it is to ease the "drug pressure" on the parasite. At the moment, heavy doses of artemisinin are pushing the malaria parasite to evolve fast. So the scientists are drastically cutting the doses of artemisinin in the area, and complementing it with a cocktail of weaker malaria drugs that in combination can have some compensatory effect. They calculate that this will reduce the evolutionary pressure on the parasite and make it revert back to type.

But Cambodia is a desperately poor country recovering from a genocide. It is impossible for them to do it alone. The World Health Organisation has stepped in with funding – but scientists are warning this project will require large and sustained funds.

The cost of not acting will be catastrophic for Africa – and, in time, we would all live to regret it. One of the most frequently anticipated effects of global warming is a spreading of the parts of the world vulnerable to malaria. The World Health Organisation has advised European governments and the Southern states of the US to take "urgent action" to prepare for "the spread of malaria" to its territory as warming accelerates. If we are going to make the planet tropical, we had better start paying attention to tropical diseases.

But this is a moment for excitement as much as despair. This is a chance to save the most precious medicine humanity has from destruction. This is a chance to save millions of people from dying "in a mountain of ice". This is a chance to do something heroic – for Africa, and for our own future. If we make this happen, we can be energised to keep on eradicating malaria, step-by-step, from the human condition: Dr Robert Koch has shown that for just $10bn over five years, we could reduce deaths from the disease to a few thousand a year. So will we seize the opportunity – or will we stand by, limp and passive, and wait for the advance of a super-charged killer?

It is not true. There is no ban. African governments can still use DDT as much as they like. Many use it in moderation for indoor spraying. But they do not see it as a magic bullet, because it is less effective than other options, like insecticide-treated bednets, because mosquitoes have developed a significant degree of resistance to it, and because it can have dangerous side-effects, like contributing to premature births and killing off local fish populations.

j.hari@independent.co.uk