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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
the anchor Edit
After stopping the nuclear threat, Mercer, having lost faith in humanity as a result of his own actions, went on a soul-searching trip around the world, hoping to find something to believe in. Unfortunately, throughout his travels, Mercer only found more and more reasons to hate humanity rather than protect it.During his travels, Mercer killed a villainous African warlord and traveled to Moscow, where he came to realize that, even though humans treated one another with decency, it was all a façade and they only cared about themselves and their individual freedoms. On his way back to the U.S., Mercer freed a small town from a drug cartel, though the citizens' celebrations only further convinced Alex that humans were selfish and not worth saving.Making his way to a lumber mill in the north, Mercer took on the alias of a writer named Jack and rented out a cabin from the mill owner Flint and his daughter Autumn, the latter of whom became attracted to him. However, Flint's former business partner, Zurich, wanted the lands around Flint's lumber mill, and when it became clear that Flint would not sell, Zurich sent two thugs to kill him and Autumn. However, Mercer killed the thugs and decided to deal with Zurich himself.
Realizing that he had developed feelings for Autumn, Mercer infiltrated Zurich's base and consumed him, discovering through his memories that Flint was once a criminal involved in many murders and extortions. Enraged and disappointed, Mercer returned to Flint's cabin and, despite Flint's insistence that he had left his past behind, killed him.
Still in disguise as Jack, Mercer returned to his cabin to find Autumn there and attempted to convince her to come with him, only to discover that Autumn had stolen his money. Autumn promptly shot Mercer in the face and revealed that her father had taught her better and that she cared about herself above anything else. To her surprise, however, Mercer regenerated and consumed her, finally deciding once and for all that humanity was worthless and that it was his duty to destroy them and usher in a new and better world.