Prototype is the term used to describe individuals who have been infected by the DX-1118 C strain of the Blacklight virus. The viral strand genetically rewrites the hosts cells, re-purposing it to suit its needs.
Due to the rapid changes caused by the virus, the infected individual does not survive the transformations. Since its creation by the scientists of Gentek, only two individuals have survived it's effects. Alex Mercer a Gentek employee and the creator of the DX-1118 C viral strand and James Heller, a former US military Sergeant. However, Mercer himself did not survive contact with the virus. Only his body remained intact. When he woke up, he was amnesiac because he was the virus himself. Alex's body is just used by that special strain of the virus, which can think and act in its own right. On the contrary, James Heller was able to survive contact with the virus without having his mind taken over (possibly due to his extremely resilient DNA).
However, during the second outbreak, Alex Mercer was able to infect individuals with a slightly different strain of the virus. These individuals were called Evolved, each with their own unique abilities. However, it was Mercer who infected Heller with his strain of the virus, suggesting that only individuals with extremely resilient (or just unique) DNA may become prototypes. Heller was apparently meant to be an evolved, given Koenig's description of himself: "I am everything you could have been; what you were supposed to be."
Alexander J. Mercer was a researcher and head of the Blacklight project at Gentek. He discovered the true nature of his work and how it was being used by his employers. In a fit of paranoia, Mercer stole a vial containing the virus while he tried to escape. However he was cornered by Blackwatch personnel at Penn Station. In a fit of rage and vengeance, Mercer broke the vial and was shot by the personnel who had cornered him, becoming infected as he died. The virus from the broken vial killed the civilians inside the station.
While he was being transported to Gentek, the virus had entered his body through his bullet wounds and rebuilt Mercer cell by cell. Later he woke up in a morgue with little to no memory of his past. With a series of incidents that followed his awakening, Mercer was able to discover more about Blackwatch and its operations than he did as an employee of Gentek.
Sgt. James Heller was a US Marine, stationed outside the US. During his time away from home, a deadly viral outbreak resulted with thousands of casualties. Heller returned home to find his family killed during the outbreak. Torn by grief and rage at his loss, Heller signs up for multiple suicide missions into the Red Zone.
On one such mission, Heller and his squad were ambushed by Mercer. Heller pursued Mercer through the streets, stabbing him repeatedly, until Alex grabbed him and infected him with his own version of the virus (dubbed the 'Mercer Virus' by the media and Blackwatch).
Powers & AbilitiesEdit
The genetic rewrite caused by the Blacklight virus evolves its host's body, giving them superhuman abilities and transforming them into deadly shapeshifting beings of nearly limitless potential, power and destruction. They can fashion portions of their bodies into weapons and cause mass devastation to the environment with their incredible superhuman physical strength and durability (to the extent of being bulletproof and unharmed from extreme impacts such as falls from any height, explosions, ect.). Newly enhanced musculature and strengthened epidermis and bodily tissue increases their strength, speed, reflexes, and agility, allowing them to break the boundaries of human sprinting and jumping ability to perform amazing parkour feats with limitless stamina.
They are also capable of self-regeneration, usually by consuming living biomass to regenerate and heal themselves, though evolution eventually allows them to heal completely without consuming. When they consume an individual, genetic memories and the DNA of the individual is retained and assimilated by a Prototype. This, paired with a Prototype's ability to mimic voice and appearance (including that of their clothing and equipment), turns a host into a potent infiltrator of almost any security.
Prototypes possess a sharpened sense of sight which allows them to see into the thermal spectrum. James Heller is shown to have a predatory sonar sense to hone in on prey from a distance. Their hearing is also heightened.
A Prototype can be identified by viral detectors, machines built to identify the level of viral contamination within an installed radius. Being a viral organism, Alex Mercer was also at one point infected with a parasite designed by Karen Parker's research team to combat the virus. The parasite was meant to create an anti-virus for Blacklight, killing Mercer in the process. This parasite spread through his body, disabling any form of offensive and defensive transformation. With the help of pathologist Bradley Ragland, Mercer was able to cure himself of this inconvience and increase his abilities further.
Eventually Blackwatch and Gentek came up with Bloodtox, an anti-Blacklight chemical mixture which was deployed throughout the city in stages. Bloodtox is poisonous to Mercer and the infected, inducing necrosis in any tissue containing the virus. Eventually, Mercer developed an immunity towards the chemical, eliminating this weakness.
While a Prototype can withstand and regenerate many injuries they will be weakened by serious injuries such as losing limbs and will need to consume something in order to fully heal; if they take too many serious injuries then they will eventually become too weak to heal themselves. 
- The term Prototype is not actually used in the games or any other media to describe Alex Mercer or James Heller, but it has been used by the fan base for lack of an official moniker to describe beings with their unique abilities as an effect of the DX-1118 C viral strain.