The President wanted immportality, so he ordered experiments on the Ultimate Life. The world's leading scientist, Professor Gerald was put in charge of it. Project Shadow was thirsly named to keep it secret. Gerald agreed, upon realizing he could use it to develop a cure for the NDIS, which his granddaughter Maria was victim to.
However, Gerald could not finish the project on his own, so he contacted the Black Comet, asking the overlord Black Doom for his help. Doom agreed on the condition that Gerald would bring him the Chaos Emeralds and their experiments produced the Biolizard. Eventually, they created the hedgehog Shadow, but Doom abandoned Gerald when the Black Comet's vist ended.
However, the project sincerly worried G.U.N., who ventured to the Space Colony ARK and found the Biolizard. Knowing it was too dangerous, they shut down the colony to keep it from falling into the wrong hands. However, Shadow was encapsulated and released to the planet by Maria.
In Shadow the Hedgehog, it was revealed that Black Doom (unsuprisingly) had his own side for aiding in the development of Project Shadow: have an agent bring him the Chaos Emeralds and use their power to warp the Black Comet to the surface and use it's powers to use the humans as a fuel source for the Black Arms. However, although Doom was sucessful in this, Super Shadow defeated him and warped the Black Comet to the ARK, where it was destroyed by the Eclipse Cannon.