I THINK I have this all planned out mostly. But, I still want y'all's opinions on this concept.
Remember how in the Mystery Dungeon games, how there aren't any humans in the world (aside from the obvious)? Me and a friend though of a solution as to why. (Remember: This is an AU from the games/manga/anime. So things might go a bit differently, also this is a very long post, so if I bore you, I apologize!)
In Hoenn, as everyone knows, in Emerald Team Aqua and Team Magma reawaken Kyogre and Groudon respectively. They go outta control and wreck havoc on the world! In their insuing fight in Sootopolis, Rayquaza appears like it does in Emerald... but, sadly, isn't able to calm them down and leaves for the skies once more.
Kyogre and Groudon continue fighting!
Eventually, their fighting gets so intense it starts to affect the other regions! Even going as far as places like Sinnoh or Unova! Eventually reaching out to the very edges of the earth itself, sending out natural disasters like meteor storms! Now, after a few years, Platinum is taking place. And we all remember Cyrus' plan: To create a whole new world in his image. A world without spirit. He summons Dialga and Palkia (and accidentally Giratina) like usual, only by summoning them, he only makes it all worse!
Dialga and Palkia, driven near insane from the power of the Red Chain, rip and tear at the fabrics of Space and Time, creating rifts in other universes and creating Gates to them! (Think Chrono Trigger only worse)
The natural disasters get even worse as cities and towns are toppled (including GoldenRod Radio Tower, where Team Rocket is invading... yeah, that won't end well...), millions of people (and Pokemon of a bit lesser extent) are killed by earthquakes, tsunamis, raging infernos, and the like. The humans, vastly dwindling in number, eventually have no choice but to go into hiding for safety to preserve their race.
Taking some of the Pokemon with them, they head down underground, making tunnels down into the depths of the earth that interconnect to all regions so as they can keep contact with eachother (People from Sinnoh go into the Sinnoh Underground, Kanto goes into the Underground Paths expanding them and going deeper, Johto goes into GoldenRod Underground doing the same thing, Unova heading down underneath Driftveil City, Hoenn going down into New Mauville enc).
Some of the Pokemon decide to stay on the surface and try to survive as best they can. Even if (like Skipper, whom waited even after he'd died in the Great Catastrophe for his "Master" to come home to Littleroot) they knew it was fruitless and possibly suicidal...
Kyogre and Groudon, after all these years of fighting, have begun to tire out. It seems neither is really winning or losing this battle. As if in responce to their chaotic battle, the landmasses of the regions have been affected greatly as if in a reverse Pangea and have conformed into one (or possibly two) large landmasses with some smaller islands still intact (Sevii Islands, Mirage Island, Seafoam Islands enc) with the rest being all sea.
Fed up with their fighting and both about to collapse, they both finally cease fighting and go deep underwater/under the earths crust to take a long rest creating the Bottomless Stormy Sea and the Magma Cave respectively (also creating the Surrounded/Miracle Sea and the Shimmer Desert among other later dubbed "Mystery Dungeons"). The natural disasters, while still around, happen less and less frequently over time.
Dialga and Palkia, having broken free of the Red Chain, have also ceased fighting and gone their separate ways, Dialga going back to the remains of Spear Pillar renaming it Temporal Tower with th remain of Sinnohs Mt. Coronet being dubbed the Hidden Land and being tucked away in the fabric of a second in time for safetys sake, it also created the Time Gears so as it would never go that crazy again. Hopefully.
Palkia making its own little space in the earth, creates Spacial Rift. Rayquaza, after witnessing the destruction of the world, vows never to go down to the earth again, and creates Sky Tower out of clouds (otherwise known as Sky Stairway).
Giratina, still resding in the Distortion World (thankfully long gotten rid of Cyrus!), creates the World Abyss, which is a place deep below the earth and is a part of the Distortion World we can actually comprehend.
Slowly, but surely, the land begins to heal itself. Pokemon feel safe for once. They rebuild some towns and cities and create their own society within this new world, claiming it as their own! They, to help Pokemon in need, start up Rescue Bases and Guilds in the name of freedom and peace! The humans are starting to relax too! Now, in secret, they send out Pokemon Trainers and Rangers to investigate this new world (and also to gather food for good measure) and see if it can ever be habitable again by humans.
Unfortunately, natural disasters ARE still happening (abit infrequently, but still pretty bad) and while it is sustainable for humans, they decide to wait a bit longer until they cease.
Just when everything seems to have been going right, a brooding menacing monster makes his appearance yet again in their world- his name is Darkrai, the Bringer of Nightmares. Tormented by his Bad Dreams ability (he will never be loved), he decides (ala Lotso from TS3) "Well, if I'm miserable, I'll make everyone else miserable too!", and thusly decides to corrupt the manifestations of Time and Space themselves, Dialga and Palkia and drive them insane! Right before this, Dialga sent out the Time Gears to different spots in the world so as they could not be taken away very easily and placed guardians at nearly every one just in case.
But, it is no use! Dialga loses his mind quickly, and time is being affected quickly as it begins to slow down and finally freeze over like ice on a pond in winter.
The world (now called the Satoshi Universe after the "famous human" every Pokemon knows and loves!) freezes over in eternal darkness as Darkrais plan is completed. With time stopped, no winds blow, the sun never rises, nobody ages, and wounds never heal.
It truly is considered the end of the world.
...But, all is not lost!
For the humans and Pokemon, they've come out of hiding and have decided enough is enough and decide to take matters into their own hands and figure out a way to stop this cataclysm! A planetary investigation team is formed, of all the trustworthy humans and Pokemon found (including a descendant of Professor Arthur Birch, who was there when the two members of the Weather Trio first went rampant, named Andy Birch, who gets teamed up with a Grovyle who was also a witness to it)and figure out a solution: They will head back in time to BEFORE this all happened and stop time from freezing by going to the past and collecting Time Gears and placing them in Temporal Tower permanently stopping the Planets Paralysis! But, they do realize that if they fiddle around with time like this, they, having come from a future that will no longer happen, will cease to exist.
So, with two members chosen (the others staying there to provide support for their world) them being Andy and the Grovyle (known as Colt), it's time to time travel! Unfortunately as of late, Andy and Colts relationship while still being good friends has started to become a little rocky. See, this isn't Colts first Trainer. Colts first Trainer (named Harold) was taken away from him several years ago (literally sucked into a Dimensional Hole!), and hasn't been seen since. Colt has always hoped and prayed he'd see hs old Trainer again, but, so far, to no avail. Colt, as of late, has been comparing Andy to Harold (or "Slick" as he was known to Colt)and Andy is not happy about it at all! Right before jumping into the Dimensional Hole, the two start to argue until it finally stops with Andy shouting at Colt (although he was just mad and didn't really mean it) "I HATE YOU!" Colt is shocked and goes silent. Colt is still mulling over this when they jump in.
Andy, now calmed down a bit, spots the shadow of Darkrai looming over them! Darkrai, not wanting his plans foiled, sends an attack to them intending to kill them! Andy, with fast reflexes, shields Colt from the attack, but in the process, lets go of Colts hand and drifts away from Colt into places unknown to Colts horror!
The time travelling trip is a success however! Colt awakens to see the sunrise for the first time in what seems like a lifetime, a sight that brings tears to his eyes, and sets off on his mission. Alone.
Andy, still alive, wakes up on a beach near a place called Treasure Town. But... as he wakes up, he realises he feels different somehow, and what's worse is that he doesn't remember anything! Not even his name! He looks down at himself and realises he's been turned into a Treecko somehow!
Having no memory of what just happened, he sets off for Treasure Town to make a new life there. Having no remembrance of his name, he gives himself a nickname- Woody, and sets up a little home for himself in the crevice of Sharpedo Bluff...
But, all is not as well as it seems, as a few months later, a nasty storm hits Treasure Town and the surrounding areas. And although their world doesn't know it, they're about to recieve some very interesting visitors! Visitors who can help save their world if they work together. Including one of those visitors who has a secret, and doesn't remember his past very well. Plus, there are problem arising in the world once again (even now, in presumedly a time of peace)... the natural disasters are rising up again, more destructive than before and driving some to insanity! The Meteor that eventually caused the destruction of the earth has returned into orbit once again! What's worse is, Time Gears are being stolen by a nefarious thief! And the Legendaries, after many years of silence, are starting to stir once more...
Can the world be saved?
Will Andy ever recover his memories?
Who is the Time Gear thief?
Who are these otherdimensional vistors?
What is the one visitors secret?
When do the events of Black and White happen?
Why am I asking you these questions when the answers are obvious?
You'll get your questions answered in the fifth tale in the Journey of Hope series... Explorers of Friendship!
...Phew! That took FOREVER to write!! Again, I'm really, really sorry if this idea seems boring/confusing/clique/stupid/overly complicated/unoriginal or any combination or option you can think of. And yes, I did say it was the fifth in the series, but, I(once they are completed) will probably post the other stories alongside this one when/if they are completed. Hopefully it won't take too long!
I'm sorry if I stole anyones ideas on this. There is quite a bit of Fanon (as they say on TV Tropes) involved as you can tell. Obviously, Andy and Colt aren't the only ones in this story, we actually have a very large cast for this one in particular! And, if it wasn't made obvious, this story WILL have a happy ending for pretty much everyone! (Yes, even Darkrai! You can tell where this is going...)
Hopefully, some of you like our idea! Tell me what you think, okay?