Project Shadow is the core of Shadow the Hedgehog's origin story. The official chronology spans the Space Colony ARK roughly fifty years before the main games, Gerald Robotnik's research, Maria Robotnik, Black Doom's involvement, the G.U.N. raid, Shadow's fifty-year sealing, Sonic Adventure 2, the 2005 Black Arms invasion, and Shadow Generations.
Professor Gerald Robotnik, described by SEGA as the world's greatest scientific mind, designed the Space Colony ARK. His research into immortality was tied to finding a treatment for his granddaughter Maria's incurable illness.
Maria Robotnik moves to the ARK for treatment. SEGA describes her as living there with Shadow and later becoming one of the most important people in his life.
SEGA's Sonic World Story chronology states that Black Doom contacts Gerald and provides his DNA in exchange for help with a planned invasion of Earth fifty years later. That DNA becomes part of the research that produces Shadow.
Gerald creates Shadow aboard the ARK. Modern official character profiles continue to identify Gerald as Shadow's creator and Shadow as the Ultimate Life Form.
SEGA's chronology records an ancient combat robot, the Gizoid, running out of control and causing major damage aboard the colony. The incident becomes one of the factors behind G.U.N.'s intervention.
G.U.N. raids the colony. Maria is killed during the incident. Her final wish and memory become central to Shadow's identity and later choices.
SEGA states that Gerald, driven mad by grief, prepares a revenge plan involving the ARK's systems and Shadow. G.U.N. imprisons Gerald and later executes him.
Shadow is held in a G.U.N. facility for fifty years. The official Sonic Adventure 2 synopsis says Dr. Eggman later awakens the top-secret weapon from that long confinement.
Eggman releases Shadow, setting the ARK revenge plan back into motion. Shadow initially acts on the altered memory of Maria's wish before ultimately helping stop the catastrophe.
Black Doom arrives with the Black Arms and demands the Chaos Emeralds. The 2005 game explores Shadow's connection to Black Doom and Project Shadow across its branching routes. SEGA's later chronology summarizes the final outcome: Shadow defeats Black Doom and decides to move forward beyond his past.
During the time-space crisis surrounding Sonic Generations, Shadow returns to the ARK and encounters Black Doom again. Maria and Gerald also appear through the distorted time-space events, forcing Shadow to confront his past once more.
Professor Gerald Robotnik created Shadow. Black Doom's DNA was part of the process according to SEGA's current official chronology, but Gerald is consistently identified as the scientist who created the Ultimate Life Form.
Gerald's work on immortality was connected to his desire to cure Maria's illness. The project later became entangled with Black Doom's bargain and G.U.N.'s intervention, turning a medical and scientific project into the foundation of the ARK tragedy and Shadow's origin.