Duke Nukem forever was all just a nightmare. After the events of the first alien invasion, the EDF takes all the merits of Duke's victories. This has meant that Duke, an outcast, has lost everything. General Graves has disappeared. After years the aliens are back for revenge but also for something else, Duke is alone and he has only Captain Dylan on his side. The EDF still needs him, Duke doesn't trust them anymore but the situation forces him to compromise that he will use his way.