With Cronus dead and the hordes suppressed, Alpha Company turns to the matter at hand. Players must now choose whether to allow Dr. Tanaka to live or die. Choosing either option will change the progression of campaign missions, but will lead to the same bosses regardless of decision.
Option A has the team sparing Tanaka's life. Out of gratitude he tells them how to slow the infestation. They must flood the Apollo ventilation system with a deadly Bio-Toxin Tanaka engineered. Doing so will kill many of the weaker zombies, and injure the stronger ones. This mission is much shorter, but involves fighting far more enemies.
Option B involves Alpha Company killing Tanaka. His crimes are too severe and he cannot be allowed to live. After his death, it is decided that the Compliance Nexus are the cause of the problem. They must taken offline, permanently. Alpha company will then have to scour the map and destroy most if not all Nexis. This mission is longer, but involves fewer enemies. However it can be tedious and requires some memorization.