Whee this will be fun!
Okay I understand that the story is supposed to sound mysterious, vague, secret, etc. but I really don't know what's going to happen in your story besides the fact that Rayquaza is going to play some part. I am assuming that trying to add grammar is something that's just not going to happen so my suggestion would be to perhaps go into more detail about what's going to happen. Yes, team rocket will "fall", but why? I really didn't get anything off of your story and I'm sure that most other people won't understand it either.
Now, looking over your screenshots, the mapping doesn't seem too bad, but then looking at the large mapshot it looks atrocious. Do you know why? There are a lot of tile errors that weren't captured in any of your screenshots. I've highlighted the ones I noticed after a quick scan.
Another thing I see in the map shot is your use of grass tiles. They're all the same tile which makes your map a lot less attractive than it could/should be. Your trees are all completely and entirely straight. This isn't always a bad thing, but when it's only one row in the middle of the town it's really less effective than it can be when used properly.
Your Route 1 screens look fairly better than this first town though it still seems rather full of ledges, the same grass tile, and blocky tall grass mapping (which again isn't a bad thing necessarily). There are a lot less tile errors in this, nice job. Tree shading is still something you may want to look at because it would make the rest of the map appear much stronger.
Haha, yes, like you said, Dersen City is by far your best map... although it's not entirely fantastic. ;)
I'm not a fan of the one-tile walking space you have by the bottom entrance so I would strongly prefer it if you would enlarge that a bit. Now I only have a few more comments related to this map. For one thing, almost all of your flowers are held up in that lower right hand corner of the map. If you spread those out more towards the left and upper parts of the map it would look much better. Also, towns should almost never have tall grass. It's just a general rule of thumb to not do that.
Oh man, it's over? :(
I want to reiterate that there's a lot of things going wrong with this hack... but it's not like there's no hope. I tried my best to point out to you what I thought could be fixed and worked on and improved and so I hope that that's how you take this criticism. Good luck with your hack, Nintendork15.