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Physically Doctor Zachary has a striking resemblence to Doctor Finitevus of the Archie comics canon, however the major difference between the two is that unlike the completely organic Doctor Finitevus Doctor Zachary is a cyborg and is noticably roboticized.
Also unlike Archie in the Sonic the Comic continuity Doctor Zachary and Knuckles are widely believed to be the last of their kind (a trait shared in-game up until Sonic Chronicles).
At first Doctor Zachary appeared as a well-mannered and gentle creature, however this was a guise to hide his true nature as a sociopathic madman who dreamt of genocidal carnage on a global scale - putting him at odds with the far more heroic Knuckles.