Alex's childhood was not rosy. Little Alex lived in a foster family in complete poverty until he was nine years old. When he was ten, his mother was released from prison, but he did not become better off from this. In fact, only his sister Dana loved him. But soon his ability to science helped him leave the not too pleasant past behind. Alex did not believe anyone, he had no friends and only cared for himself.

The only consolation for Alex was his work. After being awarded the Ph.D. in Genetics at Columbia University in New York, he was promoted to GENTEC Corporation. Alex became the head of the Black Light project. The work of Alex and his group was to create weapons from “biological specimens” sent by the government. These same “instances” were characterized by unpredictable behavior, including mimicry and the ability to “transfer” memories from the original host of the virus. Largely thanks to Alex, his group was soon able to get the most dangerous virus, whose code name was “Black Light”. Alex's incredible genetic engineering skills quickly made him a valuable GENTEC employee. His discoveries and “creations” were several years ahead of his followers and competitors. Despite his success, Alex has been the subject of increased attention of the Black Watch, a small elite army group created to confront environmental dangers. But over time, GENTEC attracted the attention of Congress. Investigations began, criminal cases began. Fearing an information leak, Black Watch decided to cover its tracks. At the same time, because of the paranoia that had been haunting him since childhood, Alex began his own investigation into GENTEC. Thanks to his sister Dana, a detective reporter, Alex found out that usually everyone involved in the Black Light was silenced by a bullet between his eyes somewhere in a dark alley.

When Alex realized that GENTEK was getting rid of everyone who knows too much, he decided to run away, fearing for his life. But Alex did not have time to escape. "Black Watch" overtook him at the Pennsylvania station. Alex understood - this is the end. Enraged, he broke an ampoule with a virus that he could take out undetected from GENTEK (he also sent Dana a huge amount of secret information via E-Mail). Mercer was killed on the spot, and in the meantime, the virus began to penetrate the blood of everyone at the station. The liquid from the broken flask penetrated the blood vessels of Mercer's body and swallowed his tissues, taking him as his first appearance, copying his body and clothes, and taking Alex's last memories as his own. The body was delivered to the GENTEC laboratory. No one then could know that while Alex's body was transported to the morgue, the virus reproduced his body cell by cell.

Prologue
Alex wakes up in a morgue on a table in front of two scientists trying to perform an autopsy, with no memory of his past. After escaping from the laboratory, Mercer discovers that his body is invulnerable even against bullets and that he has the ability to absorb other people, accepting their memories, skills and even appearance. The first victim of Alex becomes Lieutenant Charles Perry. Having swallowed it, he learns that he has a sister, a place where she lives, and that Black Watch is hunting for her. Mercer hopes that Dana has some information about what happened to him, so he finds it. However, when he comes to her house, he sees the soldiers who cordoned off her house. Having taken the form of the commander of the Black Watch, he manages to enter unnoticed. When Alex comes in and sees that a sentinel has grabbed Dana, he kills him. She was terrified of what she saw, but Alex manages to convince her to help him. Dana and Alex are moving to a safe place that belongs to Dana's friends who have left town for a year.

Dana tells Alex his own address. He arrives at his apartment and discovers a specialist certificate from the University of New York. He also sees his photo with a blonde (Karen Parker). When he touches the photo, he recalls that Karen was his girlfriend. The apartment was under surveillance. Having discovered Alex, the patrol detonates the bombs that were installed there. Alex flies out of the apartment, but, having fallen from a great height, survives. He later tracks down and absorbs the man who gave the order to detonate the bomb. Alex returns to the safe house, where Dana shows him photos of the girl in her computer.

Dana says the file has three names: Alex Mercer, Elizabeth Green and Karen Parker. The information in the file reports that Elizabeth is currently isolated in the GENTEC building. Alex, meanwhile, finds Karen Parker. Dana continues to assist Mercer in finding his goal, and Karen promises him a cure for the disease.
Betrayal Karen, finding a cure for the virus.
It soon turns out that Parker is associated with the Black Guard. When Alex comes to her for information about the collected gene material, Karen says that she lacks material and that he can find more in one of the hives. She betrays him, reporting Mercer's location to Captain Robert Cross. Cross finds Alex and tries to eliminate him, but Mercer manages to get out of the fray as a winner. However, the captain manages to inject an antivirus into him, which blocks all his abilities, except superpower, and superpowers of movement. The antivirus has turned into a parasite that eats Alex. Mercer returns to Dana, and she shows him that the patrol is watching the doctor Bradley Ragland. She also tells Alex that Ragland is a good guy, and if they can find him, he can cure Mercer. Alex admits that he absorbed many people and their feelings and memories - these are now his feelings and memories. Dana is shocked to find out what her brother has become. Mercer, meanwhile, is becoming the number one terrorist threat throughout the United States due to treacherous activities against America and its allies.

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Alex goes to Ragland, and after examining him, he reports that the bodies of the dead infected are needed to fight the parasite. Ragland asks Alex for help with researching the bodies of those killed at Penn Station. When the study was completed, Ragland hands Alex a syringe with the serum that must be injected into the Hunter, and when it works, absorb it. Alex follows Ragland's instructions and soon gets rid of the parasite and regains his abilities.

Dana's abduction, an attempt to cure Elizabeth Green.
During one of the conversations between Alex and Dana, the Leader - Hunter bursts into their apartment. He is kidnapping Dana. Alex pursues the Hunter throughout the city, but ultimately loses them. With the help of Dr. Ragland, Alex finds and eats the Leader, the Hunter, who abducted Dana. Judging by his recollections, Dana is in the main hive in the city center. Alex enters the hive where he encounters Elizabeth Green. During the fight, Alex injects Green with an antidote that could cure her of the virus. But Green's body rejects the antidote. From it, Elizabeth Green created the High Hunter. Alex defeats him and saves Dana. But the Hunter is reborn from the remaining biomass puddle. Alex brings Dan Ragland and asks him to do everything possible to save her.

Victory over Elizabeth Green, saving New York from a nuclear explosion.
Mercer sets off in search of the next target, Dr. McMullen, for whom he and Karen Parker worked for GENTEC. After that, an unknown person contacts Alex, giving him instructions and instructions. On his orders, Alex enters the base of the Black Watch and learns that the military has prepared a new “surprise” - the substance Krovotoksin, a gas that kills everything infected and harmless to healthy people. When the Black Patrol releases gas into the training room, Alex is exposed, as he was the only one who became ill from the gas. Having run away from the base, Mercer learns that he has developed immunity to Hemotoxin. But Alex has yet another battle, this time with Green herself. He lures her out of the ground with a mobile atomizer of poison. Having defeated and devoured her, he learns some details of what happened in Hope, Idaho. An unknown person announces the location of the large Bloodtoxin nebulizers and gives Alex the idea of ​​how to get to McMullen. First you need to destroy the nebulizers, and then pretend to be wounded, because for the study, his body will be sent straight to the doctor. Everything turns out to be successful and after a short conversation with Alex, McMullen commits suicide. From his story, Alex learned a lot, in particular the fact that he himself became the cause of the infection of the city, and that he was no longer a man. Alex also learns that the Black Watch is ready to hit Manhattan with a nuclear bomb as they once hit the city of Hope. Connected finally showing

After infection, each particle of Alex, including clothing, consists of viral biomass. He can manipulate this substance in any way. It is almost not breakable and has the ability to regenerate. Also regeneration is promoted by one more important skill for Alex - “eating” of living organisms. It helps to accept all the memories of the eaten, his skills and appearance. Along with the virus, Alex got superpower, super speed and extra stamina.Weapons and protection
Alex is also able to create weapons and armor from biomass that help him in difficult situations:

Claws - Alex's very first Prototype weapon. Gets it when the hunter eats. Cut the victim into pieces;
Shield - An upgrade you can buy for evolution points. Reduces enemy damage;
Sledgehammer - Another weapon in the arsenal of Alex. It is especially effective against armored vehicles;
Whip - Helps to capture a target from a distance. Can split the enemy in half;
Muscle mass - Increases Alex's muscles, which increases his strength;
Blade - A weapon similar to claws, but somewhat more effective than them. The last weapon Alex got in Prototype on the plot;
Armor - Increases overall damage resistance. In her, Alex is almost invincible. While it is activated, Alex cannot soar.
Sensory abilities
Vision of the infected - Helps to see infected creatures, indispensable if you need to distinguish the virus carrier from a healthy person.
Thermal imaging - Allows you to see objects that emit heat. Suitable for destroying targets in smoke.

Due to his difficult childhood, Alex grew up with a cold-blooded, indifferent person. When the "Black Watch" overtook him at the Pennsylvania station, he angrily broke a test tube with the virus, without thinking about the consequences. Alex also does not tolerate betrayal and lies (for example, he killed Karen Parker for betraying him.) The only person who cares about him is his sister, Dana Mercer. Even when Alex found out that Dana was helping Heller, he did not kill her, but simply locked her in a bank vault.

In the beta, Alex wore a black tank top and white sweatshirt. Later, developers changed his clothes to avoid a strong resemblance to Altair from the Assassin's Creed series of games;
Alex’s biography, posted on the game’s official website, says he has blue eyes and brown hair, although sometimes his eyes may appear gray or green. It also states that he is 5.10 feet tall and weighs 190 pounds in human form. At the time of the game, Alex is 29 years old;
For all two games, Alex has never taken off his hood. Even in the morgue he was examined without taking off his clothes. Alexa can be seen without a hood in a photograph from Karen Parker (see Gallery.);
In Prototype 2, Alex's facial features have changed a bit;
In a fight with Heller, Alex for some reason did not use the shield and armor, as well as destructive attacks and a host of other abilities, for example, glide;
It is just as strange that Heller was so easily able to tear off all of his weapons to Alex, and why Alex, who survived the atomic bomb explosion, could not restore it;
Perhaps Alpha infected (such as Alex and Green) can kill only the same alpha infected by absorption.