Shadow didn't have amnesia.
He had dissociative fugue caused by a traumatic experience.
I never felt like brain damage would make sense, because shadow can heal anything. Its more likely his body changed to avoid further suffering/try to adapt.
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(DF is a complicated disorder, hopefully no one takes this as an insult to your experience, but you're welcome to give me pointers to better showcase it in my comic if you want? He will mainly be dealing with the after effects related to depression, ptsd and general unrest, something I understand much more than DF.)
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-Shadow had DF after the ARK and that's why it was so easy to "trigger phrase" him into wanted to destroy the world.
-GUN wanted shadow to be super soldier/mind controlled/ sleeper agent, but of course Gerald didnt. (this is so meta given the time frame.)
-"bring hope to humanity" was his deactivation phrase (sonic battle).
-50 yrs later he's not remotely bothered by his past and is locked in to his new role... A role Gerald gave him during his initial fugue.
-But when he nears the final battle, Gerald inadvertently causes shadow to snap out of it and remember the real promise: Bring hope to humanity.
-His memories compounded with his current destructive behavior likely caused a secondary dissociative fugue or just reverted him back to that state. Maybe he just had a small glimpse?.
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"Shadow the hedgehog" game
-Those with dissociative fugue often impulsively wonder and travel away from home, experiencing confusion and a lost sense of self, often creating new identities.
-"Shadow the hedgehog" was a game that explores this and many endings are simply against his morals and values... because he doesnt have any. "Who am I" is very complicated and he's trying to remember his standards again.
-Doom's manipulation and twisting of his memories may have actually helped him regain them as they traveled around, which ends up being Doom's downfall.
-Over time it's possible to recover memories in bits and pieces or completely, by visiting places or discussing ones past. The trigger are partly random and often therapy is needed to find causes.
it's often followed by ptsd, depression or anger, either from the therapy finding the cause or simply the concept of forgetting everyone or feeling disconnected.
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so that's my read, it lines up and im taking it as canon. I hope at least 2 people read this lmao.