That Chancellor was a major advocate for the criminal justice system which, in 1000 A.D., went awry and lead to Crono's imprisonment. If Crono hadn't been imprisoned, he never would have found the gate to the future. Or, rather, the Entity would have facepalmed and re-located the future gate to someplace Crono would have eventually found.
Nice comic, though. I'd always smiled at the slight absurdity of putting a chancellor in a box. Twice...