In Sonic Battle, Rouge saves Shadow while they are investigating Dr. Eggman's secret base. Believing that he is a weapon, he insists the people of Earth must destroy him, but it is revealed that he ultimately has the heart and soul of Maria Robotnik and so is not the enemy of humanity. In one of Gerald Robotnik's journal entries, he mentions that "Project Shadow" was put on hold because of Project Gizoid.
In Shadow the Hedgehog, Shadow, still with no memory of his past, meets a malevolent race of aliens called the Black Arms and Black Doom, their leader, who seems to know Shadow. Throughout the game, Shadow has constant flashbacks of his past. Black Doom also baits Shadow with the knowledge of his past, while Eggman tells him that he is simply an android created by himself to mimic the real Shadow. In the final story, Black Doom reveals to him that while working on his immortality project, Gerald Robotnik contacted Black Doom and made a deal with him. If Black Doom helped him with his research, Gerald would deliver the seven Chaos Emeralds to him in fifty years' time. Using his own blood, Black Doom helped Gerald create Shadow, an immortal life form that would both help with Gerald's research and collect the Chaos Emeralds for Black Doom in the future. However, once Gerald learned of Black Doom's plot to take over the world, he created the Eclipse Cannon as...