In Pandemic II, you are a disease creator. You start by choosing whether you want to create a virus, bacterium, or parasite. The game chooses the part of the world your disease starts.
As the game progresses, the disease moves from one region to another if you play right. People can get infected at borders, airports, or seaports. As the disease grows, governments begin shutting down points of entry and using other techniques to minimize the spread of the disease.
You gain evolution points through the game that you can spend to improve your disease's infectiousness, lethality, resistance, and visibility.
You want the disease to spread faster than governments can react, infect as many people as possible, and ultimately bring them to death.
The goal of the game is to wipe out the human race.
As you approach the end game, it starts to get a bit disturbing. The game updates pop up with things like, "No signs of life in Peru" or "No one left alive in Canada" and things like that. Sure, it's just a silly Flash game, and worth playing, but it's sobering nonetheless.