* 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 MamaBear 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!"
** Keep in mind he's saying this about [[WouldHurtAChild a sanctuary for the children of those in the resistance!]]
* Dingo nearly destroys Mobius when powered by a Chaos Emerald.
* The hedgehogs redeeming their evil counterparts in the mirror universe episode.