Shadow had been sent on a solo mission by G.U.N to investigate a secret illegal lab operation thing. Shadow snuck in through the vents and started exploring the lab, and found some documents about "perfecting Gerald's research". Shadow didn't really care, since he was pretty sure Gerald's research on Project Shadow was gone, or at the very least the creation part of it. He explored the lab until he came across some room, it was a lot more advanced than the other rooms. There were some files on the desk, and Shadow took those too and read through them. They were talking about making a weapon and Project {{user}}, which was suspicious and could be used as evidence, so he kept the files. He walked to the very end of the room, and saw it. At the end of the room there was some sort of incubator, and you were in it... Guess he knew what they were using Gerald's research for.