Below is what one of these individual islands might look like on the overmap, where you choose missions.
Note: This story will be slightly tweaked depending on if you're Cool Corps or Pretty Committee, but the major "plot points" of the story should be the same.
The CC/PC were all hanging out one day, when they heard the sound of candy wrappers rustling down in the Candy Basement. They ran downstairs to look, and they saw that weirdo Steve Jenkins grabbing all their candy and stealing it! They tried to stop him, but they weren't quick enough, the sly dog got away.
They realized they NEEDED to get this candy back, so they decided to go on an adventure, find Steve Jenkins, kill him, and bring home the candy. Problem is, he lives in Monster Island which is far, far away. So they needed to take a boat, but they did not have one, so they went and asked the locals if they can borrow their ferry. They're told that they may borrow it, but only if they first defeat the local Undead infestation.
They defeat the Undead champion, Skull-a-copter, and take the ferry. They're warned that the ferry cannot travel too far, so they should stop and refuel at a nearby island called Crabby Caves. As soon as they get there, though, they see that the blasted PC/CC was also on the way to take out Steve Jenkins. Obviously if they do it they're gonna take YOUR candy, and you can't have that, so they MUST be destroyed!
They destroy the other party, and move on. You're forced to make a stop at Ant-Arctica, and [some story shit] but eventually you kill all the damn gross bugs here, and move on to the final island, and then kill the monster party & Steve Jenkins, and retrive your precious candy.
First Island - Green Island
This is the first battle in the game, and so it's mostly open, and quite easy. There is a secret down at the bottom containing a +1 Sword.
This town has a chance to tell you about S1, a secret level which connects via 3. You can also learn about Clarence the Assassin who has been locked up on A2.
After beating Battle 4, both a1 and 5 become available.
If you beat this level, you are rewarded with Clarence the Assassin, who is a really strong, fast melee Hero unit.
This is a timed mission, and it's rather difficult, but it's exceptionally difficult if you reach the secret area that unlocks S2.
Final Battle (8)
Here you battle Captain Skeletonne and her minions. Beating this moves you to the next island.
Second Island - Pyramid Land
This should be a Desert-themed island, lots of open space and mountains, marked by BUG PEOPLE.
Third Island - Cold & Snowy
This is a winter-themed level, making movement harder for most units - monsters include Snowmen, Abomominable Snow Monsters, Icecube-Heads, Cold People
Fourth Island - Foresty Forest
This is all very dense woods and brush, making spotting a huge deal. Monsters are typical High Fantasy monsters like Ogres and Goblins.