Everyone is focusing on the crystals, but what about the comets?
The comets are not on the English logo either. Here's a crazy theory:
There are two evil teams, unlike Magma and Aqua, they don't interfere with each other, but still compete. Their goals are to draw this comet into Earth's orbit, because there is a legendary waiting inside.( the box art ones) or some great power. but I'm sticking with legends for now.
Anyway, the evil teams( who would at one point have been one team), would have secretly been in kalos during the events of X and Y. After Lysandre fails, they sneak into the ruins and examine the ultimate weapon,they obviously can't bring it with them, but they realize that they can recreate it with materials they have back in their region. They return to their region and begin to have disputes within the organization, as to what they should do. There would be two comets approaching the planet. Each contain the mascot legend. In one version one of the two teams uses their version of the weapon to shoot down one in the comets. The next few years they focus on building the ultimate weapon in secret. Then using the ultimate weapon( or something else( which is probably likely)), they use it's power for their true intentions. your character would be fighting an admin and because of the battle, coordinates are inputed wrong and they shoot the wrong comet. In sun they shoot the one that has the moon legendary, and in moon, they do manage to hit the sun one.
now would be a good time to describe the base. Their version of the ultimate weapon would look nothing like the original one. Using modern technology, they were able to make a telescope that contains the power of the weapon. Maybe using those crystals? The evil team bases would be in an observatory. So the telescope would be big but not like the ultimate weapon.
Now moving on. The evil team leader will reveal that the ultimate weapon originally created Deoxys( like the fan theory). The mutation that it caused on that meteorite was spread when it broke into space. Over time, it created two more powerful legends from the mystic power of a comet. The sun and moon ones.
This beings began to help control the sun and moon, and protect Earth from their comets. However the ultimate weapon was used to attract them to the planet like deoxys. Afterwards, we would learn that the being is approaching some sacred site in the region. You need to get there immediately, as the evil team departs.
For the next bit of time in the game, the comet will be approaching the planet faster and faster.
You see news reports of how the comet is cause destruction through the region. you see a news report of fires in multiple parts of the region( that are blocked off for now), such as the area on the way to the 8th gym. This is where we see the fire department rush to put out the flames, hence the concept art.( more just me wishing.hoping, but you never know) We see people being injured and taken in the ambulances. The region would then call for a hero! As you make your way towards this location, you would also learn that the moon is coming closer to the planet, which throws off the tide system, and water levels begin to rise, with flooding closer to the coast.( cue amazing 3d cutscene showing these effects) You finally make your way to this sacred place.( Maybe a tower or something?) Fighting your way through grunts and admins. You make it to the top, with the other evil team's help. Who would reveal that they almost went forward with their plan, but then the saw the effects of the other team, and realized how wrong they'd be. They come to your aid, knowing only you can save the world, as they help you get to the top and then give you the masterball.
In a non 3d cutscene, you learn more about both the legends, and how the world is doomed if they are taking out of balance. The team that didn't awaken the legendary, will discuss some ancient tale( in a full 3d cutscene) of how ancient tribes did the same thing many years ago. And tell how wrong they were in this. They warn the evil team leader about how dangerous the pokemon they just awoken was.
The evil leader passes it off as false and talks about how they can use to enforce order in the world if they control it, as they can take out anyone at any time with the natural disruptions the pokemon causes. The members of the team that didn't awaken the legend, tell you how it's all up to you now to save them.
As you approach, the comet finally crashes down into the ocean near the tower. The evil team leader looks down as the legendary awakens. ( this is after one last battle with them, before it rises up from the ocean) The leader calls the legend, and talks about how powerful they could be together. The legend rejects them and with one strong attack, knocks the leader out and sends them across the floor. You then engage it in battle.
This came out really long, but the plot just flowed to me as I pondered over the comets.
Probably won't happen, but thoughts?
