One thing I've noticed is that there are lots of things unexplained in this story, namely what the decon actually is, what an alimon is, and how the residents of your valley know who Cj is.
One of the worst things a writer can do is to start a story assuming that the reader knows everything you do about it, and work from there. Things can get very confusing very fast.
Other then that try to start with the Gang in all of the LBT stories, because its a very healthy platform to begin building your story on. Everyone knows who Littlefoot, Cera, Ducky, Spike, and Petrie are, so you don't need to explain them right away. From there you introduce your new characters, and build on that foundation.
Chapter 1 for example, features Lance, Cj and Ace (three characters we don't know and have never heard of) murdering an innocent swimmer out of hatred to the valley (we don't know why) and defeating Topsy without breaking stride (something not even a sharptooth could do). An alternative way you could have written this chapter - if I might make a humble suggestion - would have been to introduce the gang first, and then bring in your OC villians and describe them how the gang percieves them, which is the point of view the reader can relate to.
A few modest structural improvements and I can see this story being a good one.
