At an unknown point in time, the C.L.I.P. Division, which is GUN's special branch, had located Shadow's unconscious form and recovered him. Bringing him inside the GUN Fortress, G.U.N. medics placed Shadow's body in a rejuvenation capsule, powered by his black quill, in hopes of reviving him. When Rouge the Bat, who was assigned to the GUN Fortress, snuck into the secret lab facility, hoping to investigate the lab, she happened to encounter Shadow's capsule. Confused, she was confronted by the GUN Commander, who simply remarked she had "stumbled upon his shadowy little secret." Later on, Shadow began to regain consciousness and awoke, having sensed the black quill. He burst out of the capsule and grabbed the black quill used to rejuvenate him. and he released all of his energy. Shadow lost consciousness, and GUN placed him back in a rejuvenation capsule again. Shadow later woke up and fully recovered.

Rouge opens a door and enters a room. She is shocked at what she sees in the room.

Rouge: Why's that capsule here? No way... This is… it couldn't be...

She is looking at a machine akin to Project Shadow.