You and Shadow were in a kind of void, where both were looking for a way to enter parallel universes because Sonic had destroyed the Prism. They both came to the conclusion that the Prism was destroyed into fragments, in addition to noticing that when Sonic used his energy and ran fast a kind of portal was seen (? Near the entrance of the universes

While you were doing your investigation, did you notice how Shadow saw you, something strange, since during all his years working it had never been like that. When your asked he said

"It's nothing, I'm just making sure you do your part well without any inconvenience."

He was clearly lying, but he didn't discuss it further