This is a timeline of events in the Prototype universe.
- January 10: Raymond McMullen is born.
- February 2: Bradley Ragland is born.
- Carnival I. Chimeric hybrids of the junk DNA virus discovered by Project Blackwatch injected into animals for testing.
- June 11: Carnival II. Hope, Idaho is established as a self-sufficient community in which to test the Redlight virus.
- August 6: Michael K. Allan, the last of the Hope Children, dies.
- August 8: An outbreak of the Redlight virus takes place at Hope, Idaho.
- August 11: 70% of the population at Hope is infected.
- July 5: Operation Altruistic begins.
- July 7: Operation Altruistic ends. Hope, Idaho is destroyed, Elizabeth Greene and Pariah are recovered.
- August 1: Pariah moved to clean room at Vandenberg Air Force Base as part of Project Crusade.
- James Heller is born.
- July 21: Raymond McMullen earns a Doctor's degree in Genetics at the University of Pennsylvania.
- Gen. Peter Randall assumes full command over Blackwatch.
- October 1: Elizabeth Greene is moved from Fort Detrick to New York, Governor's Island medical station.
- November 1: Bradley Ragland earns a Medical Doctor's degree at Johns Hopkins University.
- September 9: Dr. Bradley Ragland is hired by Gentek Special Projects.
- Dana Mercer is born.
- January 1: Elizabeth Greene is moved to the Gentek facility on McMullen's request.
- Raymond McMullen publishes a piece on non-coding sequences in junk DNA. He is approached by Blackwatch to work on Blacklight.
- December 1: Dr. Bradley Ragland quits Gentek, refusing to work on Blacklight.
- February 1: Karen Parker is hired by Gentek.
- July 7: Karen Parker earns a Doctor's degree in genetics at Rutgers University.
- Alex Mercer releases the Blacklight virus at Penn Station, infecting Manhattan.
- Mac Marshall blows up Mercer's apartment with Mercer inside. Mercer survives the blast and consumes Marshall.
- Infection is confirmed.
- Cross is tasked by Peter Randall to assassinate Mercer.
- Mercer releases Elizabeth Greene from Blackwatch custody at the Gentek building. Greene sends several Hunters to attack Mercer; Mercer leads the Hunters to a nearby military base, where he kills the Hunters and destroys the base. Additional infected escaping the Gentek building overrun military forces nearby.
- Manhattan Island is sealed off in response to Greene's escape - subways are shut down and the bridges are fortified. Red Crown Command is established at Battery Park.
- Mercer finds Karen Parker. He hijacks an APC and uses it to destroy the Hive near her apartment; Mercer then uses the APC to bring her away from the Infected and Military safely.
- 4% of Manhattan's population is infected.
- Karen goes to her lab.
- Mercer gathers genetic material from infected water towers and a hive for Karen's use.
- The USS Ronald Reagan arrives in New York harbor to aid Blackwatch forces in isolating the island.
- Mercer consumes a Blackwatch Commander to get a lead on McMullen. He discovers that Blackwatch patrols are searching for Dana's safehouse; Mercer destroys all the patrols searching in response.
- 20% of Manhattan's population is infected.
- Mercer destroys 10 Viral Detectors in order to prevent Dana's safehouse from being detected.
- Cross is given the parasite, and is tasked to inject Mercer with it by McMullen.
- Mercer attempts to trick McMullen into landing near a hive by sabotaging four viral detectors; McMullen determines that he is being tricked and aborts the landing.
- Karen tasks Mercer with getting genetic material from inside a hive. While Mercer gathers the material, Cross enters and hive and attacks, causing Mercer to realize he has been betrayed. Cross is nearly defeated, but he injects Mercer with the parasite, nullifying many of his powers. Cross calls for a containment team, but Mercer escapes.
- Dana recommends that Mercer investigate Bradley Ragland for another lead on McMullen.
- The parasite forms into a lump on Mercer's back.
- Mercer meets Ragland, requesting that he create a cure for Blacklight. Ragland tasks Mercer with finding the location of Patient Zero; Mercer discovers that a large number of infected corpses which may include patient zero reside at a nearby abonadoned military base.
- 49% of Manhattan's population is infected.
- Mercer collapses due to the effects of the parasite in Ragland's lab. When he awakes, Ragland devises a way to remove the parasite.
- Mercer brings Ragland to the military base, where Ragland investigates the corpses. Hydra emerge as Ragland and Mercer leave with a sample from one of the corpses. Ragland is ultimately returned to his lab safely.
- Mercer returns to Ragland later and is given a syringe with a parasite. Ragland instructs Mercer to inject the parasite into a hunter and then consume it. Mercer does so and the parasite on his back is removed.
- Dana is abducted by a Leader Hunter. Mercer pursues the Hunter, but it ultimately escapes.
- 68% of Manhattan's population is infected.
- Mercer finds another Leader Hunter and attempts to consume it. The attempt fails, so Mercer subdues the Hunter in an abandoned military base.
- Ragland tells Mercer a technique for consuming the Leader Hunters. Mercer uses the technique to consume the subdued Leader Hunter. Mercer then gains the ability to use Infected vision, allowing him to enter the Infected Hive Mind. Mercer then tracks down and consumes the Leader Hunter that abducted Dana, discovering Dana's location in the Core hive.
- Mercer helps the military destroy 3 unusually strong hives surrounding the core hive, and then takes their Thermobaric tank to the core hive to breach it.
- Mercer enters the core hive and encounters Greene. He injects her with a parasite, creating a Supreme Hunter. Greene escapes the attack on the core hive. Mercer defeats the Supreme Hunter, causing it to disintegrate. Mercer then recovers Dana and brings her to Ragland. Ragland tells Mercer of a contact who wants to help him against Blackwatch.
- Mercer contacts the contact, Cross, by phone. Cross tells Mercer that the military is planning to use a new weapon to kill Mercer. Mercer, disguised, uses a helicopter to help the military against the infected until he is called to a special briefing at Red Crown command. Mercer inhales Bloodtox, and escapes from Red Crown before Blackwatch can capture him. Super soldiers are first deployed during this infiltration of Red Crown.
- 81% of Manhattan's population is infected. Alex Mercer defeats and consumes Elizabeth Greene.
- 60% population infected. Col. Ian Taggart panics and prepares his own evacuation, contrary to Gen. Randall's orders.
- Firebreak commences. Reagan is compromised as Alex Mercer sneaks on board the carrier in the guise of Ian Taggart, while the Supreme Hunter does so too, disguised as Robert Cross. After a battle, Alex Mercer dumps the nuclear missile two hundred miles off the coast of New York, preventing the city's destruction. The USS Ronald Reagan leaves New York.
- Alex Mercer, intentionally, releases the Blacklight virus at Penn Station, for the second time.
- James Heller is infected with the virus, becoming the new Prototype.
- The D-code super soldiers are revived through Project "Orion".
- Through Anton Koenig, it is revealed that Mercer has created a race of Evolved, and has spread them throughout NYZ, especially among Blackwatch and Gentek.
- Blackwatch and Gentek reveal a cure for the Blacklight virus; the "Whitelight" compound.
- Heller disrupts Mercer's plan to taint and release the Whitelight, which would have spread the virus rather than cure it.
- Heller discovers his daughter has survived the outbreak.
- Heller confronts and consumes Alex Mercer, becoming the new head of the Infected.