Following is a list of events that take place in Prototype 2. These events take place in New York City, now known as New York Zero (NYZ), following Sgt. James Heller's vengeance against Alex Mercer, after having lost everything and everyone he loved to the Blacklight virus.

Yellow Zone

• Meet Your Maker
• Resurrection
• The Strong Survive
• Operation Flytrap
• Brain Drain
• Project Long Shadow
• The Lab Rat
• Feeding Time
• Salvation
• The Mad Scientist
• Phase Two
• Natural Selection
• The Airbridge
• Enemies and Allies

Green Zone

• A Stranger Among Us
• The White Light
• A Nest of Vipers
• Taking the Castle
• A Maze of Blood
• Alpha Wolf
• Fall from Grace
• The Descent
• Predator and Prey

Red Zone

• Burned from Memory
• Last Resort
• Fly in the Ointment
• Divine Intervention
• Operation Firehawk
• Lost in the System
• A Labor of Love
• Murder Your Maker