With the widespread fall of communism in the early 1990s, neoconservatives of various stripes joined in the celebration of the winning out of western democracies. Many neoconservatives had felt they were in the Truman-Kennedy camp of foreign policy vision and it had in large respect won out to New Left prescriptions for civil co-existence with the Soviet Union. Francis Fukuyama's "The End of History and the Last Man" argued that human progress in government largely culminated to western liberal democracies. This contradicted Marxist doctrine, which presumed that History (writ large) would "end" with the fall of capitalism, the enactment of socialism, and the creation of Communism.
Much of neoconservatism rested on the assumption that the great conflict of modern civilization was between the democratic way of life and socialism and communism. Without that great enemy about, neoconservatism kind of entered a transitional phase. Irving Kristol sought to more or less have U.S. Foreign policy retract from the world once more, embracing a more ardently realist perspective. Over the next several years, however, his son would have different ideas. William Kristol and Robert Kagan, along with several other figures in the previous fight came together to redefine America's purpose in the late 20th and early 21st centuries. They didn't want to be called "neoconservative" because they had always, more or less, been conservatives and hadn't had that "left to right" transition that their parents did, and, on top of that, neoconservatives became identified with the Cold War which was now over. They called themselves "neo-Reaganites" and followed a modified form of Scoop Democrat philosophy. More hawkish than most realists and liberals alike, but valuing human rights and the virtues of democracy, these neo-Reaganites would take advantage of the "unipolar moment" by being the big brother of the world, ready to defend the helpless against the perceived enemies of the western world and American interests. Prime on their list included: Iraq, Iran, North Korea, and China. Though often they disagreed with one another, this group had a much more cohesive vision for a policy movement than most neoconservatives previously had.
Meanwhile the old dogs of the neoconservative movement focused their attention toward the culture wars of the 1990s and celebrated, to a large extent, the victory of their ideas in the GOP. Many neoconservatives felt that nihilism had taken hold of American life and it needed to be rectified by a renewed dialogue and respect for traditional institutions, including religion. Irving Kristol became more ideological and more connected with the Republican Party in demanding that the religious right be featured prominently in America's fight to "redeem" itself. Less ideologically, John Diullio Jr. Became one of the most prominent figures of the bi-partisan push to establish greater coordination and collaboration with religious entities to help ameliorate some of the problems facing American citizens. Realizing that government workers did not always have the best prospects for helping a family than, for instance, their local church, Diulio and others pushed hard to make religious institutions less the enemy of the state and more of a partner. Diulio was not a religious fanatic, and often complained about staffers in the Bush administration who were more partisan and punitive to perceived enemies of the religious right, but he understood that with proper protections in place to stop religious groups from using federal dollars to convert people, these already-existing community institutions could help administer a number of social services. Though initially controversial despite the bi-partisan effort, the office survives to this day and was somewhat thriving in the Obama administration.
But neoconservatism soon became almost entirely associated with the Bush administration's foreign policy after 9/11, despite the protestations of Nathan Glazer (and later Francis Fukuyama).