Duke is called into action via the Government, aliens have once again landed and are wreaking havoc. Duke pummels the alien menace through the streets of New York with the help of some marines, and eventually to the Statue of Liberty. Here, Duke discovers the aliens true plan, to go back in time, mess with historic events so Earth now wouldn't be what it is, they could easily take over. However, Duke in his fight, is teleported to the future, where the aliens have won and the humans are near extinction. In this time zone, Duke battles through horrors of new alien breeds in the future, and the zombified corpses of those who didn't survive the fallout. Duke eventually meets up with the small band of resistance fighters in the old headquarters of the U.S. army in New York. There, they tell him that the aliens are indeed screwing with history, so much that this future is just one, if Duke wants the old one back he'll have to fight for it. The humans have developed their own time machine in order to send a soldier back to re-write history, and destroy the aliens. Duke is sent back to the Old West, where aliens have messed with the American West in an effort to mine out Earth for its resources.