I plan to continue the story line to the levels of Sonic & Knuckles, because they are essentially following the plot of Sonic 3 & Knuckles. As for what will happen after that, I don't know. It seems so far in the future that I don't know if I'll even still be publishing the comic by then.
A bit of advice, you should try to find the Mystical Forest Sprites, it's a forum that has a bunch of sprite projects, including a much better Amy sprite sheet (as in higher quality sprites). It also has a new Ultimate Sonic S3&K Sheet, which includes many helpful new poses and parts. I do have some warnings though, you need to sign up to the forum in order to see it, and you can't really search for topics, so you'll have to look around a bit.