MEP would work by the trainer and pokemon activating there mega stones. Trainers and Pokemon would where the stones on there rings. Rings made to harness the power.
How ever, this fell out of hands and fell into blocks. Then was hidden all over the world. New world gen. was found after this. They where like strongholds with one per map. Some Stones are mined, from Ancient statues. Stupid traders sold the stones like diamonds, stolen form pokemon. These stones came form every where.
One man knew about this. He stole many stones them has weapons. He attacked every one in the minecraft world out side of battle using moves of destruction and death. That man would of had forever power after capturing Arceus but one thing was harmed to much. The world.
That man build him self a base. In his own world in a area of Anti matter, pass Time and Space, with cooled Ground and heated Oceans and stolen SKY. To stop this man you need the rulers of those he mocked to find him. Then you would need to get up to battle him wile he is attacking you on his Mega pokemon. Then will you be aloud to challenge him. If you win then you will earn your mega stone and Flute! But Untill then a Challenge of Utimate power awaits....
(This is an Idea I have for pixlemon. After you Capture Dialga, Palkia, Groundon, Kyogre, Giratina, and Rayquaza with all in your party, they will lead you to a Prime Boss NPC. First he will tell you a similar story to the one up there. Like bosses In Pokemon. Next you will need to get him in battle wile his pokemon are fighting you as a trainer. When you find the boss you can battle his team of Meags. As a reward you will get a mega ring and Flute. Then wake up in bed like if it were a dream.
next time you summon Your Lengendary team. They will take you to the same place. Spearpiller. Play the Flute and you will see Arceus. Now you may see Arceus in the wild..... unless you do /Pokegive Codes188 Arceus 100 s you hacker!