They are corporations, building up everything. What is not made by one is made by the other. Even the pokeballs and the medicine is made by them, and the button of the balls have a little logo on them.
They basically own the region...but aside from wanting to block out the other team they want more then the islands they're on...and conveniently my region is made to be near the center of all of the rest of the pokemon world and connected to all the other regions via ancient undersea tunnels made by the 4 secondary legendary pokemon (you know, the secondary ones like the Tapus and the Beasts and that) They are fighting for control of those tunnels and then control of the world. Each of them will have connections to other evil teams in other regions, and they will be joining in.
My region is the Butterfly Region and the 2 main legendaries are butterflies, and some of the head scientists are working on time travel because the plot will revolves around the butterfly affect somehow (I'm still working on that) So once you, the hero, realize what they are up to you will attempt to stop them by going back in time to stop them from forming.
Unfortunately, by stopping 1 of the 2 teams from forming you give the 2nd team the power to rule...and you only realize this to late. Whichever team that you end up stopping was the main one you were fighting the whole time, so the opposite team rises to power. This leaves you a bit unprepared because you're used to fighting the other team.
The other thing with my region is that there are 3 possible starting towns and thus 3 sets of possible starter pokemon and they're all on different parts of the region (It starts with you moving there and all 3 professors are trying to figure out where it would be best for you to live, so you take a little quiz and based on the results you end up in either Fieldveiw, Tropica, or SeaBreeze) Depending upon where you start will depend on how you encounter them 1st, but you will end up in all of the situations regardless
If you start in FieldVeiw you 1st meet whichever team because they are terrorizing the bug types the town is known for, looking to hopefully just...run into the legendaries (cuz they're bugs) Admittedly these 5 grunts aren't the smartest, and the leader of the team even tells you "yeah, I didn't tell them to do that, they just kind of decided to and I didn't care enough to stop them"
In SeaBreeze you will find them attempting to catch a very high level Gyarados and....failing miserably...this is where you will learn that the organizations are actually both split in 2, with the very lovely side and the evil side, both having completely separate names and logos for obvious reasons that are obvious (still working on the separate names tho) and both having separate HQs that are connected by more secret tunnels. It is forbidden for grunts to ever be seen in the HQ of the front company until later. We'll come back to that.
In Tropica you will find the head scientists of the other team there, studying the pokemon for the front company. The majority of the pokemon around Tropica are oddly colored, similar to the Orange Island pokemon. This is because they are somewhat isolated within a large, lush tropical jungle. Most of the pokemon there are to strong for starting trainers to catch, which is why the prof. gives you great balls to start with instead of normal ones. In this case, the main team you will be fighting against appears to try and stop the other team's scientist and steal their research and you, believing that these are normal scientists, must stop the evil team.
About 3/4ths through the game the teams will stage a fight against...themselves, prepared and willing to loose to you. See, by that point you are starting to get suspicious that the team and the front company are one in the same, so they make the team grunts invade the HQ building of the front company. The hero, suddenly convinced that they were wrong and they wouldn't possibly invade themselves, launch an attack against the enemy team, save the head of the front company which is also the leader of the evil team, and leave...none the wiser.
Also, I know I want your main rivals to end up being the son and daughter of the leaders of the evil teams. There will be only 2, and neither of them will be aware the other is the rival to their parents. In fact, only the daughter will be aware of their family. The son was removed from the situation by his mother and grew up not knowing who his father is. The daughter is planning to follow in the footsteps of her mother and father, with her mother being the head and her father being 2nd in command, but 1st she has decided to compete in the league under cover, in hopes of becoming champ and making the team's task much easier.
There is also going to be an undercover agent from whatever team you're not fighting that ends up being your friend. You find it odd that they keep appearing near where attacks happen but, then again, you also keep appearing where attacks happen. The only things that could possibly be a hint other then that is that they are wearing team colors: Black and Gold or Black and Red. But, you may also be wearing those colors and several others are wearing those colors. They are trying to help you, but this is mostly because you are causing a problem for the opposite team.
This is...what I have figured out so far...