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.
- 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.
- Day 01: Infection confirmed, Mercer escapes from Gentek morgue, first Marines arrive at Manhattan Island.
- Day 03: Mercer releases Elizabeth Greene from Blackwatch custody at the Gentek building. The Manhattan Island is sealed off in response - subways are shut down and the bridges fortified.
- Day 04: 4% population infected. USS Ronald Reagan arrives in New York harbor to aid Blackwatch forces in isolating the island. Red Crown Command is established at Battery Park.
- Day 6: 20% population infected.
- Day 8: 49% population infected. Robert Cross injects Mercer with a Parasite, but Mercer manages to find a cure for it.
- Day 10: 68% population infected.
- Day 12: 81% population infected. Alex Mercer defeats and consumes Elizabeth Greene.
- Day 15: 60% population infected. Col. Ian Taggart panics and prepares his own evacuation, contrary to Gen. Randall's orders.
- Day 18: 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.