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Prototype 2 is a comic series consisting of three books detailing the events that occurred between, Prototype and Prototype 2. The series was announced on January 17, 2012 as a collaboration between Dark Horse Comics and Radical Entertainment. 
The story for this series has been written by Dan Jolley, who has also scripted Prototype 2. Each comic has been illustrated by different artists. The first entry, "The Anchor", has been illustrated by Paco Diaz. It continues the journey of Alex Mercer after the events of Prototype.
The second book, "The Survivors", is illustrated by Chris Staggs and follows a small group of residents of New York trying to escape the city after it has been transformed into NYZ with the outbreak of the Blacklight virus. Victor Drujiniu has illustrated the last book, "The Labyrinth" provides a deeper backstory and acts as a prologue to the events of Prototype 2.
The books were released bi-weekly and were split into two parts.
- Prototype 2: "The Anchor"
- Part 1: February 15, 2012
- Part 2: February 29, 2012
- Prototype 2: "The Survivors"
- Part 1: March 15, 2012
- Part 2: March 28, 2012
- Prototype 2: "The Labyrinth"
- Part 1: April 11, 2012
- Part 2: April 25, 2012