Following is a list of events that take place in Prototype. These events were the result of Alex Mercer's search for his lost memories and the truth behind the creation of the Blacklight virus.

Episode 1

• Memory in Death
• Unexpected Family

Episode 2

• Past and Present
• Behind the Glass

Episode 3

• The Wheels of Chance
• A New Order

Episode 4

• Open Conspiracy
• In the Web
• The Altered World
• Errand Boy

Episode 5

• Confessions
• Under the Knife
• The Stolen Body
• Biological Imperative

Episode 6

• The Door in the Wall
• First and Last Things
• The First Monster
• Making the Future
• Children of Blacklight

Episode 7

• Men Like Gods
• A Dream of Armageddon
• The World Set Free

Episode 8

• Things to Come
• On Instinct
• Shock and Awe

Episode 9

• The Last Man
• Two Tickets

Episode 10

• One Thousand Suns