A loosely interconnected Islamist uprising is spreading from Syria in northern Arabia to Mali in West Africa and threatens to produce terrorism in Europe and the US. That is the clear and immediate danger. But the Western response to it may signal the demise of the American-led global prescription which followed the end of the Cold War in 1989. Washington proclaimed democracy, human rights and the free market. But from now on those values may be trumped by one simple demand: security.

When the West shifted its position on President Assad of Syria the new message was clear: “If you are on our side in the fight against global jihad then we do not mind who you are or what you do.” In other words, 25 years after the collapse of the Soviet Union, we are back in a new global war in which the absolute need to win trumps our basic values.

The Cold War was a political competition for the loyalty of nation states, a race for military superiority on a global scale and also an ideological competition between capitalist and state-run systems. Every aspect of life was seen through the lens of this struggle for world supremacy between two ideologies, expressed most clearly in the nuclear arms race between them.

It was total. During the Cuban Missile Crisis in 1962 when the Cold War nearly became hot, I was at school. When the deadline for removal of the Russian missiles from Cuba approached, lessons were abandoned and we were herded into the chapel to pray for peace. It felt as if the end of week might be the end of the world.

The West’s peaceful triumph over the Soviet Union meant the American prescription for the world’s nation states could spread through most of the planet. These values have been powerful, though rarely all-powerful, factors in global governance ever since.

Eastern Europe embraced them more or less successfully. In South America, Asia and Africa, the US stopped supporting military dictators and encouraged real elections to take place. China was the one big exception. It allows the market to rule the economy but, to this day, it cracks down on human rights and democratic movements that might threaten the absolute control of the Communist Party.

For Africa the Americans announced the new prescription in April 1990 and President Mitterand followed suit at the Francophone summit at the La Baule conference in June. Britain left it to the Foreign Secretary, Douglas Hurd, whose language was far woollier. Britain, he said, would favour “countries tending towards pluralism, public accountability, respect for the rule of law, human rights and market principles.”

Throughout Francophone Africa great national debates began, involving what has come to be called “˜civil society’ and the politicians. France also felt able to push for free elections in its former African colonies. So did Britain – though more circumspectly. Elections were organised – much to the distress of presidents who had been faithful followers of France or Britain and now felt betrayed. Even in little Togo the protesters took on the army in the streets and pushed them back into the barracks (although President Eyadema managed to stay in power in the end.)

In Anglophone countries too there were uprisings demanding free and fair elections. In Zambia President Kenneth Kaunda held an election, lost it and stepped down. In Kenya, where the British High Commissioner had never met leading political figures opposed to President Daniel arap Moi, there was an opposition rally demanding elections. The police broke it up and that resulted in more than a week of rioting and mass arrests. But eventually a free election was held (which Moi won) and the British High Commissioner finally met opposition leaders.

More important than the elections themselves was the opening up of political space for the press and civil society organisations at a local level. At a pan African level the adoption of a new African Union charter outlawed coups. Since then the AU record on election monitoring has been dismal but it has maintained a good record of not accepting anyone who comes to power through the gun. This, however, may be pure self-interest. If they allow even one coup, it sets a precedent and who knows who might be the next victim?

Presidents began to learn how to survive elections and use the full panoply of the state to win. The police and army became their rally organisers, the presidential helicopter their transport to rallies and the national budget could be used to buy off areas that felt excluded.

So how much has international action and opinion affected elections in Africa? The most prominent activity of outsiders has been election funding and monitoring although monitors have rarely managed to catch more than a whiff of vote rigging or ballot box stuffing. That is usually done subtly in Africa – Nigeria is the exception – so monitors can only point to inexplicable anomalies rather than hard evidence. External funding channelled to particular candidates by other governments, African or non-African, has been difficult to pinpoint.

Human rights in most of Africa have certainly improved. Opposition parties may not have the financial resources of ruling ones but they can speak out more forcefully than before 1989 almost everywhere in Africa. In countries like Kenya, Ghana and Senegal the free market rules and there is real competition for votes. Ironically two countries which are among the most successful economically, Ethiopia and Rwanda, rejected the democracy and human rights agenda. Their “˜free market’ is also very state controlled. Is there a connection?  Will they – rather than, say, freewheeling Kenya – become the model for Africa?

In the battle against Islamist militants the Obama administration, unwilling to put US boots on the ground, is increasingly using local allies and their forces to fight the insurgents. Washington will say that this war protects our freedoms and of course, if the stark choice is between the US and the Islamic State, there is no argument. But in this struggle more and more powers will be given to hugely expanded and US-backed security services. Generals who are backed by the US military may become more powerful than presidents. Human rights and freedom of speech will be increasingly restricted. Privacy is invaded. Truth suppressed. Torture ignored and permitted.

Increasingly the way in which the global battle against Islamism is being fought will trump the values for which the West proclaims to stand.

Richard Dowden is Director of the Royal African Society and author of Africa; altered states, ordinary miracles. Follow Richard on twitter@DowdenAfrica