The Yamato Server disappears after the X-Virus attacks, and the Doom Server has taken it's place. It's up to the you and up to 3 of your friends, the Digital Security Guard (D.S.G.) to venture into the Doom Server, discover the source of the virus and deal with the infection before it can infect the Home server.

You will venture into the Dry Lands stop the virus from spreading, into the Venom Jungle to stop the Dread Note from launching and then the Machine Pit to destroy the final boss.

After finishing the game for the first time, you unlock Hard mode, where the enemies are stronger, but you keep all of your levels, equipment and digivolutions. Do it again, and you unlock the hardest difficulty, Very Hard.