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The explanation you gave quite frankly didn't show how it wasn't. Joining GUN does not suddenly make him protecting the people of the earth, doing what he normally does ass shown in STH's canon ending makes him protect Maria's promise. Letting the past go is not going to suddenly make him especially with how Shadow is as a character join the same agency that's done the previous things I've mentioned to him. No, it's not clear and I'll explain perfectly why. I present you this johnny video perfectly explaining what's wrong with linking previous Sonic games to 06.Them knowing each other doessn't suddenly make past adventures apart of the loop.