Metal Eye 2 is set in the same sci-fi universe and is closely related story-wise to the first game. In the future, people have built the floating city Zeron, where the best scientists work on creating androids, artificial human beings who look the same way as real ones. Harness Technology is the biggest company that creates androids. The hero of the game is a scientist named Wirg, the father of the first game's protagonist. His work is to train the androids after they have been created. One day, soldiers come to his friend's house and try to detain them for disclosure of secret information, and Wirg has to escape. He is saved by a nun and brought into a small town in the middle of wasteland, where his adventure begins.

[Edited from Moby Games]