Æon Flux

In 2011, a deadly pathogenic virus has killed 99% of the Earth's population, forcing the survivors to regroup and scatter across the Earth.

404 years later, in late 2415, all of the survivors inhabit Bregna, a walled futuristic city-state, which is ruled by a congress of scientists. Although Bregna is largely an idyllic place in the destroyed Earth, people routinely disappear and the population suffers from nightmares. Read more on Wikipedia.