Project Shadow (プロジェクト・シャドウ, Purojekuto Shadō) was a medical research programme conducted by the United Federation fifty years before the main events of the Sonic Pokémon series. It produced both Biolizard and Shadow the Hedgehog, as well as indirectly causing the death of Gerald Robotnik. The Project's legacy forms the basis for the storyline of Sonic Pokémon Adventure 2 Arc and, to a lesser extent, Black Arms Arc.
Initially conceived by the President of the United Federation as a means of researching immortality, Project Shadow was thusly named so as to remind the researchers of the need for absolute secrecy in their work. Professor Gerald Robotnik, "one of the most brilliant minds of all time", was assigned as the project leader. Despite his initial reluctance in conducting research of this nature (claiming that it "crossed Man's limits"), Robotnik realized he might be able to co-opt the program in order to find a cure for Neuro-Immuno Deficiency Syndrome, a fatal disease afflicting his granddaughter, Maria.
As the Project progressed on the Space Colony ARK, Gerald made contact with an alien life-form called Black Doom, the leader of the Black Arms race. Doom assisted Gerald with his research, going so far as to provide genetic material for the Project in the form of his blood. Gerald also studied the Chaos Emeralds, producing Chaos Drives to test infinite energy of the Emeralds on living tissue. The Project produced Biolizard, a creature containing many of the desired traits: regeneration, restoration, self-reproduction. However, it required a life support machine to remain viable. In addition, the Biolizard also grew at a rate that even he did not expect—gaining a size of 2.7 meters and 350kg in just a couple of days. The Biolizard likewise, possessed a low learning rate at that time, making it more comparable to an animal; was sensitive to temperature changes; and at the time of the report was not strong enough to walk, although its tail and neck were strong. It also contained an organ that was installed into it to start the Chaos Control.
Gerald's fantastic (though incomplete) successes prompted fear in the military hierarchy of G.U.N., however. The Biolizard proved difficult to control, and the army leaders, distrustful of Project Shadow as a whole, conspired to shut the research down. G.U.N. manufactured a purported biohazard catastrophe on the space colony, using this as a premise to evacuate the ARK's population and arrest anyone involved in Project Shadow, aside from Gerald himself, whom they would use as a scapegoat for the "accident". Shadow the Hedgehog, Project Shadow's latest live product, was ejected to the planet by Maria during the raid, but was later captured and sealed away by G.U.N. forces.
In the Black Arms Arc, it is revealed that Black Doom had his own, non-humanitarian agenda in contributing to Project Shadow. While the President wanted immortality and Gerald wanted a cure for NIDS, Black Doom intended the program to produce an agent who would gather the Chaos Emeralds for him on the inner solar system, 50 years later. In this, Doom is actually the only one to get what he wanted from Project Shadow–although it backfires spectacularly on him, in that Shadow, despite delivering the Emeralds, goes on to become Super Shadow and defeat Devil Doom, while the ARK's Eclipse Cannon obliterates the Black Comet entirely.