I know a lot of people don't know this...but I actually have a good pile of gijinka-Sonic stories. Though they started with a short 7-page yaoi comic done on a dare, I actually went through and solidified up the universe and made it something more than a thing started on a dare.

My gijinka-universe essentially follows the video games, starting with "Sonic Adventure" (though older game events are referred to, sometimes)...where the titanic clash between Sonic and Perfect Chaos had a "wave of mysterious energy" ripple over the world and altered all of the Anthros into humanoid forms. (So, yes...they became humanoid through a story event.) While some adjusted easily (like Tails), others had a harder time (like Knuckles)...and poor Shadow woke up with a form very different than the one he was in when he was put in cryogenic stasis.

Confused by his jumbled memories of what happened 50 years ago, adjusting to a new form...whether he should take revenge or not...this is what Shadow had to deal with upon waking. And remembering Maria and how she died...probably was what made him hate humans and want revenge. (There is a point in SA2 where Shadow IS crying over his memories of Maria...this is meant to be based on that moment.)

Shadow the Hedgehog belongs to Sega, this gijinka/humanoid form is my own design.