I feel this could have been a little better. Could at least note that for those who haven't watched the series yet that they need to use the space bar to move along the text boxes. Story seems to be good anyways.
The graphics are all sprites except Shi the demon hedgehog who is a custom sprite that you have noted Milan0077 made .In my opinion though it looks kind of dull, not saying Shi is a completely dull character but, way, way too many spikes on their head. Made less on their head so it looks cleaner. Everything else here seemed to be rather fine though.
The story seems to be the Mario Bros. are hunting for stars and yet the Bully revealed at the end is going to prevent them from doing so by sending many minions and the such their way. Then Shi came, first in an Organization XIII cloak then suddenly appears without it. Could possibly made the cloak a little shorter and seem bigger on the top to show he has a lot of spikes too. Shi finally gets destroyed with a knock to the head.
The music used seemed pretty good for the most part too. Although the guitar loop used early on for when they were meeting Shi seemed a little unfitting. Could have used some dark sound piano tune instead.
The dialogue boxes could also maybe be done a little different since I noticed a lot of "..." used during some of them and in a couple of other dialogue boxes, the text stretches past the text box limit in the flash.
Overall, not too bad, could use a bit of improving though with how Shi looked.