The Murasaki-Wigglytuff Edition (carbon age-1,000,000y)
So  it came to pass that the roof of the world was painted with stars, just  as the earth was coated with the plants and animals of the land, the  oceans were filled with the vibrant life of the sea, and the sky was  completed by the creatures of the air. And Arceus saw that it was good.  Yet the world still felt uncomplete and unfinished. The Pokemon of the  world, however, were shiftless and lazy, and budged only at Arceus’  command.
So  Arceus said,”Let there be a dawn of spirit in this pure new world. Let  free will, thought, and emotion come to the creatures of the earth, the  seas, and the sky!” Three beings came forth to represent Arceus’ hope,  and he named them Azelf, Uxie, and Mespirit. The pokemon came alive as  never before, and Arceus saw that it was good.
After  a time, Arceus grew weary of enforcing the rules he wanted his world to  have himself. So Arceus said, “Let there be three laws that shall  ensure that my will will come to pass for all time in this world that I  have created.” And it was so.
The  first law drove all living things on forward, never allowing them to  halt their progress, but allowing them to look back at their lives.  Arceus named this one Dialga.
The  second law kept living things apart, but brought them together at the  same time, so that they could better praise Arceus. Arceus named this  one Palkia.
The  third law set an end for each and every mortal being, such that they  would be removed from the earth, the sea, and the skies in their time  and join Arceus in the land of the gods. Arceus named this one Giratina.  
Then  Arceus spoke. “Let the three laws live and breathe as every other being  for all of time, such that my influence will remain in this world long  after I retire.” And it was so. The three gained draconic bodies inset  with diamonds, pearls, and opals. 
But  soon Dialga grew tired of watching over all time. He asked Arceus,”The  others only have to watch what is going on now. I must stand over all of  time in the earth, the seas, and the skies, and ensure its progress.  Would it be so unreasonable to grant me a partner that could assist me  in keeping the world ticking?”
Arceus  agreed. So he said,”May another being be created to aid Dialga in his  task.” Arceus named this being Celebi, and she aided him in the care of  time. Arceus saw that it was good. Yet he remembered the battles of  Groudon and Kyogre, and thus warned Dialga,”If she shall encourage you  in any action not becoming of your heavenly role, I shall hold you both  responsible.”
Years  later, the pokemon of the world had grown to large numbers, and were  playing with, mating with, and hunting each other, as pokemon will. And  Giratina came to Arceus, and he said,”I cannot distinguish the sleeping  and the departed from each other. Would you grant me an assistant, such  that I may deliver to you only those who have finished their time in the  earth, the seas, and the skies?”
Arceus agreed. So he said,”May another being be created to sort the sleeping from the dead.”
He  named the being Darkrai, and he aided Giratina in the separation of the  living and the dead. But, remembering the battles of the earth and the  sea, he warned Giratina,”If he shall encourage you in any action not  becoming of your heavenly role, I shall hold you both responsible.”
Years  later, when those who craved power had gained it, shoving aside the  weak, Palkia came to Arceus. He said,”Each day I look down upon the  space you have put under my control, as you bade me do. But today I  looked away, for I could not watch the suffering of the innocents and  yet have no power to intervene. It sickens me, Lord.”
“One  cannot be both a law and an arbiter of the law. To allow you to rule  space and at the same time interfere with the doings of the living  beings of the world would be an abomination.”
And  Palkia said,”You have given the others assistants to aide them in your  holy work. However, space is simple, and I need no help to keep all  beings together and apart as you have decreed. May I then have a being  to remind the weak and the mourning in the earth, the seas, and the sky  below that there is still hope, such that they may continue with their  worldly lives, and enter your care in their time with peace and  contentment and without fear?”
Arceus said,”That is too big a task for even myself. I cannot cure unhappyness.”
And  Palkia responded,”For a single being, you are correct, my lord. So  create a hundred! Or a thousand! And let them go out and spread the joy  and happiness that you can bring, in hopes that they may inspire hope  and belief in you!” Before Arceus could respond, these beings appeared  on a mountain, the sacred meeting place of the earth and the sky.  Astonished, Arceus named the beings Shaymin, and adorned them with  heavenly flowers that granted them wings.
Arceus  said,”Palkia, your hope and your faith has made your dreams real. May  it happen to many others as my world grows.” Then he turned to the  Shaymin collected before him. “Go forth, and spread my joy to the  desperate, the mourners, and the weak! Give hope to the meek, the  sickly, and the weak of heart!” Most of the Shaymin took flight on their  wings and spread around the earth, the seas, and the sky, but a few  remained. These Arceus tasked to maintain a safe home for their tired  brethren to return to. 
And Arceus saw that it was good.
Present (June 21st, 235 CRE)
3:35 PM
Hoenn Route 119
Skarm
Altaria  struggled to bear both of our weight through the driving winds and  torrential rains. Its wings thrashed against the air, desperately trying  to make it to safer ground
“Altaria,  we need to get across the river before they start shooting! You can do  it!” Winona urged her bird on, but it wasn’t enough.
“We  aren’t going to make it!” Just below us, the river loomed large.  Swollen tides began to rise up onto the banks, and the falls downriver  would put an end to us if we didn’t drown. Altaria’s breathing was  growing ragged, and she let out a shrill cry as her wings gave out.
We  crashed down in the river, and the current yanked at my clothes, trying  to drag me away. The shore was close, so I swam for it and dragged  myself up the bank, Winona gasping for air behind me. 
“Let’s  go! They’re not far behind!” I grabbed Winona’s wrist and turned for  the woods, but she wouldn’t move. “Come ON! We have to go!”
“No! Altaria can’t swim! I’m not going to let her drown!”
“Just withdraw her!”
“I can’t! When we crashed, her pokeball got smashed on a rock! It’s broken!”
“If  we don’t get out of here, we’re----” Altaria’s cry filled the air, and  Winona’s hand left mine. “Wait! WAIT!” Winona splashed back into the  water behind me. On the opposite bank, I could just make out Magma men  dashing out of the Weather Institute, their assault rifles cocked. “DAMN  IT!”
Winona
I  dove headfirst into the raging river, towards where I last saw  Altaria’s head break the surface. Across the river, I could hear the  Magma men mobilizing-wouldn’t be long until they crossed the river at  the bridge upstream to hunt us.
Altaria  cried out, and I saw her break the surface again startlingly far  downstream. Turning downstream with the current sped me up a bit, but I  didn’t know if it would be enough. My arms flailed against the  floodtides, and Altaria popped up again, just out of my reach. With a  final spurt of energy, I wrapped my arms around her blue neck and  dragged her head above the surface, where she gasped for air. 
I  started kicking for shore, but I wasn’t making much progress. Altaria  was around 50 pounds on land, but she was much heavier in the water with  her cottony wings saturated. And her wings dragged against the current,  pulling us closer to the waterfall with every moment. Altaria’s skin  glowed red, maybe from stress, maybe from the fire that pulsed in her  heart, maybe something else, I didn’t know. 
The  shore was so close now. My feet brushed against the sand and I kicked  forward with new strength. “Come on, Altaria, come on, we’re almost  out.” I dragged her out onto the muddy river bank and then collapsed on  my back alongside her, exhausted.
Skarm
On  the river shoreline, I tried to keep up with Winona and Altaria. The  current seemed to pick up pace the further it flowed, and I was tiring.  Behind me, red glowing flares soared up above the river where we had  landed, revealing nothing. 
Finally, I saw Winona dragging Altaria out of the water in a somewhat clear stretch of the shore. 
“Winona!  I ran over to her and yanked her to her feet. “We have to go! Now!” The  Magma soldiers fired more flares over the river, and one of them  settled and began drifting downwards in the rain over our heads, bathing  everything in an eerie red glow. 
“Okay...okay...Skarm, grab Altaria’s other wing, right at the joint. Let’s get her into the woods.”
“We  don’t have time for this!” I helped her carry Altaria anyways,  expecting a bullet in the back any second. Gunshots rang out from the  other side of the river, and the bullets buried themselves in the mud  around us. “Go! GO!”
Together,  we bore Altaria’s deadweight on our shoulders and sprinted for the  treeline. A few steps away, Winona stumbled, and Altaria went down with  her. “Skarm! I’m hit!” 
“We’re  almost there!” I tossed Altaria the last few steps and dove into the  forest. A few seconds later, Winona crawled in behind me. 
“Where?  Where are you hit?” Under the trees with the clouds overhead, it was  pitch black. Winona and Altaria were silouettes in the darkness, but  each lighting strike let me see them better for a split second.
“Twice.”  she groaned. “Left arm, right calf.” I saw a rip in her sleeve, and  peeled it back to try to see the wound. A volley of lightning strikes  gave me enough time to see a red line cut into Winona’s arm that was  slowly spreading to her jacket. But from the angle they were shooting  from, there was no way they could have penetrated through the outside of  her arm.
“Your  arm’s fine, just grazed you. We should still try to bandage it though.  Let’s see the leg.” I rolled up her sleeve as the thunder answered the  lightning. The radio buzzed. “Can’t believe this thing is still  working.”
“Magma,  listen up. Our two loose ends are in the woods on the opposite side of  the river from Whiskey Irene. Sweep the forest and eliminate them. Also,  it might be good for some of you to know that your jobs are on the line  here. And if you’re not one of us, but you’ve seen what we’ve  done...you become a loose end. Get it done. Reshiram out.”
“Well,  that’s nice and cheery.” Winona quipped while I waited for a lighting  strike. One finally came, and it wasn’t pretty. The bullet hole was  slowly oozing blood, and I could see cracked bone when I looked into the  hole.
“Your leg is hurt pretty bad. Looks like the bullet embedded itself in the bone.”
“Well,  we’re pretty fucked then, aren’t we? We’re 10 miles from Fortree, in  the middle of a FUCKING THUNDERSTORM, the Magma men are after us, and I  can’t walk. What the fuck are we gonna do?”
“First,  I’m gonna bandage you up-mind if I take a bit of your jacket? Then,  we’re gonna get the hell out of here. We’ll walk to a road and flag  someone down.” 
“I don’t think I can walk, but I’ll try...AGHHHHH!”
“Okay...okay...I  got you...I got you...” I slid my arm under Winona’s, taking the weight  off her right leg. “We gotta get out of here.” 
“If  we wait until the storm ends, Altaria and my Skarmory can fly us out.  But it’s not safe for them to carry anything as big as us while it’s  pouring like this.” We hobbled off into the woods together, followed by  Altaria hopping a few steps at a time. Minutes passed as we struggled to  make progress in the pitch black forest.
A few minutes later
The  radio chirped again. “Reshiram, we’ve reached the site where we last  saw the loose ends. Echo Team found blood stains on some leaves.”
“Excellent  progress. All teams, form a perimeter around the nearest roads. Echo  team, proceed with disposal of the loose ends. Reshiram out.”
“Well,  that’s not good.” I tried to pick up the pace, but I ended up dragging  Winona more then helping her walk. “Let’s take a quick break before we  keep going.” We sat down in the mud behind a fallen tree, where a little  light filtered down through the tree tops and the rainclouds.
“How’s  your leg doing?” I pulled out my miraculously intact water bottle and  offered Winona a sip, which she gratefully accepted.
“Could be better. You have any idea when this storm is gonna end?”
“From the radar last night, it looked like it was gonna rain like this all day.”
“Great. Just great.”
“Well,  cheer up. At least we have each other, and we’re not dead yet.” I  leaned in towards her, and we kissed. It probably would have been better  if one of us wasn’t slowly bleeding out into the mud. 
“Reshiram, this is Entei. We’ve spotted two teenagers kissing, blood trail seems to lead right to them. Permission to engage?”
I pushed away from Winona’s lips. “Damn!” I whispered.
“Permission granted. Echo team, load up and approach with caution.”
“You know, Skarm, just once before they kill us both, I want to kiss you without getting interrupted.”
“Doesn’t  look like we’re gonna get much of a chance to do that.” Altaria had  started to get agitated, and it appeared to be looking behind us. “Get  down!” I threw myself on top of Winona just before bullets slapped into  the fallen tree.
“They’re on to us!”
“Roger that, Entei. They’re unarmed except for their pokemon. Just make sure they go down. Reshiram out.”
“Skarm, get off me, get on the ground!”
“We need to get moving!”
“Just  do it now! Altaria, Flamethrower them!” I dropped to the ground, and  searing air battered my back as Altaria delivered a stream of blue fire  to the Magma grunts. I heard screams from the distance, and I knew she  had found her mark. 
“I  think you overdid it a little!” I yelled as Altaria closed its mouth.  The blue flames vanished, replaced by red and orange ones where she had  aimed. “You started a damn wildfire!” I sprinted into the burning area,  and bent down towards one of the soldiers. 
“Skarm, what are you doing!”
“Getting  some intel.” I picked up the phone, flicked the slider, and it sprung  open. Then I returned to Winona, coughing thanks to the smoke.
“We’re out of here, let’s go. And couldn’t you have not started a fire?”
“I thought the wood was soaked enough that it wouldn’t burn!”
“Well, now all the other guys have a nice beacon telling them where we are!”
“Echo  team, report! Come in, Entei! Alright, all teams, converge on the fire  in the woods. Shoot anyone who’s not in a Magma uniform.”
“Run!” Winona shouted. I helped her to her feet and started off away from the fire. 
“Wait, wait...what did you pick up?”
“A phone.”
“Why don’t you use it? We could get some help!” 
“I  don’t know who could help us. We’re miles out of town, and the police  don’t give a shit anyways. I could try the fire department, thanks to  your Altaria.”
“Okay. Dial 222 for the fire dispatchers.”
“Fortree Fire Department, what is your emergency?”
“I’m calling from the woods near the Weather Institute. There’s a wildfire.”
“Fires in that area are natural this time of year. They help to clear out old growth and make way for new trees.”
“You should come at least drop some water. There are people in the area, and the fire is uncontrolled. It could spread.”
“The rain should handle it better then we can.” The woman hung up.
“DAMN IT!” 
“Nothing?”
“Zilch. I can already hear Magma closing in.”
“Anyone else? I mean ANYONE, no matter how ridiculous the idea is.”
“There  is one.” It was probably was the last person on earth I’d want to call  while hanging out with Winona, but if we had to get out of here...
I dialed. The phone rang twice.
“Hi, this is May. Who’s calling?”