Prototype takes place in modern times. Alex awakes in a morgue and sets off to find out what has happened to him and moreso to seek revenge on those that are responsible for turning him into the Prototype. Traveling through the heavily populated New York City, with all the people, sites and scenes from New York, the twisted plot of what has happened and what is about to happen is played out. Alex becomes involved with the battle between the Blackwatch Military Special forces, who are actively trying to capture or terminate Mr. Mercer, and the viral outbreak known as the Infected. Prototype sends Alex on a unique anti hero quest for retribution and possible salvation as he unfolds and seeks answers about a 40 plus year conspiracy in the making.

Who do you believe and who is on Alex's side? As the game progresses, you will experience twist after twist, and it leaves you wondering if the only character you can believe in is yourself. The story is put together well and it doesn't get too complicated or blown out of proportion. It is actually well developed and although some will liken it to the Resident Evil storyline, it does have its own variations on the story and the abilities and design of the main character are way more intricate than the majority of "biologically altered or conflicted" storylines in other games. To find out where this elaborate story goes, turn the lights out, turn the volume up, and be ready to be thrust into an ever evolving and changing storyline.