- The hedgehogs wrecking Robotnik's Floating Fortress.
- Sleet and Dingo steal a Chaos Emerald from Robotnik and plan to control Mobius with it.
- The three-part story arcs were quite good; one featured Knuckles in a lead role.
- Any time Aleena goes into Mama Bear mode.
- In a call back to a Sonic SatAM plot, one episode has Robotnik challenge Sonic to a race. Sonia and Manic, figuring Sonic couldn't resist, show up to try and rescue him... except he knew it was a trap and didn't show, and they have to be rescued.
- Bartleby Mink setting aside his aristocratic lifestyle to defy Robotnik near the end of the series.
- Robotnik has an awesomely evil line in "Tangled Webs":
Dr. Robotnik: When we find it, "Sanctuary" will become... "Cemetery!"
- Dingo nearly destroys Mobius when powered by a Chaos Emerald. This, might I add, was about ten years before Sonic Adventure.
- The hedgehogs redeeming their evil counterparts in the mirror universe episode.