I'll do this according to the way you divided your story and as I finish reading each parted the story.
Let me start with the exposition. From the look of stuff it seems as a combination of the Sonic Movie (1996) with Sonic been isolated with Tails on an island, your current knowledge on the comics, as you introduced Angel Island and the Death Egg in the exposition, (as from the videogames I don't have much knowledge on that). This reminds me of the Martian School of writers who wrote poetry in viewing the world as an extraterrestrial alien which was very hard for them as they knew their world; you are doing almost the same as you know what the comics contain on each issue, yet you're viewing it as if you didn't know what was in them. As for diction, the descriptive word "vagabond" for Sonic seemed at first a bit on the negative side if one was to define it on its connotation (as most readers would do), but you have your reasons, as maybe this Sonic will be different from the comics as you chapters develop. All that said, the panoramic method you use gives enough background information for a reader (with no knowledge on the Sonic world) to allocate what has happened and what is happening.
As for the story,
The first part contain a good description of the setting thru imagery and personification. The description of Sonic's attire is well developed. The way you made Sonic just enter the base and just dropping his thing in a random room makes him seem carefree and somewhat arrogant. Also, by Sonic's saying "Typical, I come by, and no one's around to greet me" may show that he's previous adventures have started like this "typical"; a good way to put background information thru dialogue.
The second part. You kept the description of setting at the great level, allowing the reader to follow with the changes of setting; you gave necessary info on the Swatbots and Robotropolis, which is great as you didn't leave the reader to guessing how thins may look like. You introduced characters at a steady and descriptive pace without revealing their names, this makes the reader wonder and want to read more to know the names. Also, thru the dialogue you were able to portray the attitude of the characters, and also thru actions such as Robotnik's. Towards the end of this part you introduced both Sally and Tails effectively.
The third part. Wow. This part seem like the rising action, and your realistic style. Good place to introduce Antoine's and Rotor's name as well as the youth of Sonic, (I was wondering at the beginning of how old you were going to portray him), you didn't made the reader wait for plot to elapse. As for the action, it came quickly into the story as well as the endangerment of two characters, a good way to keep the reader entertained. Also, the way you made the characters escape the trouble is believable and realistic. At this point you have gotten my full attention.
Part four. Bravo, you introduced more background info on Robotnik, and you it looks like you know very well how each character speaks and the dialogue they use. And once again, at the verge of defeat you managed to have an exit at the right moment. Most importantly you kept in mind the 'domino' effect that the bombs could cause as well as the concept of powerful toxins killing the FF.
Part five. Hmm. Sonic's epiphany at Sally can be seen as a comic relief. A very good cliffhanger with not revealing Tails' purpose in joining the Knothole FF to the reader.
Overall. Well it looks like the story will be in third person limited, as only Sonic's thought are revealed and the persona seems to be centered on Sonic. There were some minimal tautology and grammatical errors, which I disregard, for as you said you're just practicing your writing. In conclusion, well I must say that that this continuity seems legit and very interesting, I'm looking forward to reading your other stories on this creative writing. Hope these is of help.