The continuous 30 levels are divided into four areas; UAC Underground, UAC's Starport (Hellish Outpost), City, and Hell.
Immediately following the events in Doom, the player once again assumes the role of the unnamed space marine. After defeating the demon invasion of the Mars moon bases and returning from Hell (the manifestation of Hell where the Deimos moon floats over), Doomguy finds that Earth has also been invaded by the demons, who have killed billions of people.
The humans who survived the attack have developed a plan to build massive spaceships which will carry the remaining survivors into space. Once the ships are ready, the survivors prepare to evacuate Earth. Unfortunately, Earth's only ground spaceport gets taken over by the demons, who place a flame barrier over it, preventing any ships from leaving. The marine then battles hordes of demons and is able to deactivate the force field, allowing the remaining humans to escape. Once all the survivors escape Earth, the marine is the only human left on the planet.
Just as he sits down to await death, knowing that he saved mankind, the marine then receives an off-planet transmission from the survivors in orbit, who have managed to find out where the armies of Hell are coming from. The message reveals that the demonic base is in the center of the marine's own hometown. He then fights through the city until he reaches the base, but sees there is no way to stop the invasion on that side. He then decides to step into the portal to try deactivating it from the other side, entering Hell (a different Hell than the one that the Deimos moon floats over in the first Doom).
After fighting through the hordes of Hell, the marine reaches the location of the biggest demon he has ever seen, called the Icon of Sin (Baphomet). He kills the Icon of Sin by firing rockets into its exposed brain. Its death causes devastation on Hell, and the portal to Earth has been sealed. Now with Hell defeated, the marine joins with the other humans in an effort to rebuild and restore life on Earth.