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Project: Shadow was a project put forward by the Republic of Station Square to make immortality possible. The project was held on the Space Colony ARK and the leading scientist behind it was Professor Gerald Robotnik, who wished to use the project as a means help cure his granddaughter, Maria Robotnik, of her Neuro-Immuno Deficiency Syndrome. In order to break some barriers in his research, Gerald asked the leader of the Black Arm race, Black Doom, to assist him. With his help, Gerald was able to create Shadow the Hedgehog, an immortal being with Black Doom's skills in Chaos Control.
In return for helping him, Doom wanted Project: Shadow made into a weapon as well for him to use, but Gerald turned the project into a champion for Mobius to protect it from Black Doom and his race when they returned in fifty years to collect Shadow. Gerald eventually managed to create an immortal life form known as Shadow the Hedgehog as well as an over-sized prototype. When Station Square's military became aware of Project: Shadow's success, they decided to use Shadow for themselves as a weapon.
But when they sent soldiers up to take hold of Project: Shadow, Maria caught sight of them and informed her grandfather about it. Gerald told her to take Shadow to the escape pods. She did this successfully, but was shot in the back when she tried to escape herself. Gerald was then brought back down to Mobius, where the military informed him of his granddaughter's death and ordered him to create a new Project: Shadow on Prison Island.
The military managed to find the original Shadow and Gerald managed to reprogram him to take revenge on the planet for killing Maria, who had been Shadow's only friend on the ARK. Although Gerald complied and attempted to make a new Shadow, the military couldn't tell if he was trying to "pull a fast one" due to Shadow being so advanced and had Gerald executed. (StH: #98, #157, #171, SU: #2)
Fifty years later, Gerald's grandson's alternate counterpart, Dr. Eggman, stumbled upon Shadow who was sealed in stasis on Prison Island. Eggman then released Shadow and attempted to use his power to take over the world, but Shadow later rebelled after he watched a video aboard the ARK and temporarily allied himself with Eggman's greatest enemy, Sonic, in order to save the world and came close to sacrificing himself to do it, but he was saved by a group of aliens known as the Bem. Roughly a year after these events, Shadow joined the Guardian Units of the Nation in order to better fulfill his purpose as Mobius's protector. (StH: #98, #124, #182, SU: #2)