NegaMetallix

Did that take place in the game's universe..?

Nope. Some of the references did though. I know that much

They're considering it a sequel to the game. The black comet came around again and they want to destroy it before it reaches earth. I don't know how much they plan on referencing the game, but if you haven't played it, essentially Shadows part alien because the original alien leader that was in the first black comet helped Dr.Robotniks grandfather create Shadow, so he has some of the aliens abilities.