As Doomed Again is a remake of Doom 1 and 2, the episodes and levels tend to follow the same storyline, but the levels themselves are not remakes of the original ones. In most cases, their layouts have nothing do with the originals'.

EPISODE 1: KNEE-DEEP IN THE DEAD
"You're a marine, one of Earth's toughest..."
Well, you know the story. Back to Phobos where it all started.

• E1M1 - Entryway
  
• E1M2 - Nuclear plant
• E1M3 - Hangar
• E1M4 - Toxin refinery
• E1M5 - Command Control
  
• E1M6 - Phobos Lab
  
• E1M7 - Computer Station
• E1M8 - Military Base
  
• E1M9 - Phobos Anomaly

EPISODE 2: THE SHORES OF HELL
"It stinks like rotten meat, but looks like the lost Deimos base..."

• E2M1 - Deimos anomaly
  
• E2M2 - Containment Area
  
• E2M3 - Refinery
• E2M4 - Command Center
• E2M5 - Deimos Lab
  
• E2M6 - Spawning Vats
• E2M7 - Halls of the Damned
• E2M8 - Fortress of Mystery
  
• E2M9 - Tower of Babel