Rather than the player playing through three related episodes as in the first Doom, gameplay takes place over 32 levels (two of which are secret levels that can be accessed from level 15), albeit with interludes for when the story develops. Due to the larger and more complicated maps with larger groups of monsters, the game had somewhat higher system requirements than the original.

However, because the levels are nonlinear players can wander off the beaten path, and those that do are often rewarded with bonuses, like health pickups and more powerful weapons.

As with its predecessor, Doom II's levels can be completed in a straightforward fashion. Levels are completed by finding an exit, whether it be a switch or a teleporter the goal is simply to advance to the next area. Each level is infested with demons that can be killed with a variety of weapons that can be picked up throughout the game. The game still consists of the player navigating large nonlinear levels. Instead, the development team took advantage of advances in computer hardware since the release of the original game that allowed them to do more with their game engine by making much larger and more intricate levels. There were no major technological developments, graphical improvements, or substantial gameplay changes. Doom II was not dramatically different from its predecessor.

Doom 2 map 28