_X_ TIME SKIP
'Thoughts'
"Telepathy"
The Shore line of Kanto and Johto, once filled with laughter of people and Pokémon, now were silent with the bodies of the Alliance Soldiers that came ashore on D-Day. The Alliance Army pushed through the defenses to avenge those killed in the attacks at sea. Ash and John stood on the shore line looking at the bodies as they were all gathered and given proper respect. That was when Bonnie joined them and shivered at the amount of bodies on the shore. She then said, "I think we all have seen enough bloodshed for 3 lifetimes." Ash nodded his head as John said, "Yeah, any word on CHili?" Bonnie smiled and said, "The Shrapnel from the ship didn't sever any main arteries nor did he need to get his leg cut off, he's gonna pull through."
John smiled as Ash said, "Thank Arceus." Ash then looked at their map and said, "our sources say that Tracy made the Indigo Plateau a fortress, Vermillion City's his capital." Ash then asked, "Pallet town will probably be a fall back point for his army, what's left of it that is." Soon Gary came up to them and said, "We just heard, A new Region joined the fight for freedom, it's called the Cornera Region. They're sending their armies to join us." John smiled as Ash said, "Good to hear that we'll be getting reinforcements." Then John said, "But are they necessary? I mean we have all the regions liberated except for Kanto and Johto." Ash looked at him and said, "Honestly John, the more members we have, the more protected the Otron Region will be." John nodded his head before they were told Tracy fled Vermillion City and went to Pallet town.
John and Ash looked at each other and nodded their heads, this had been a long time coming so they decided to take on Tracy themselves. Ash looked at Gary and said, "Gary, I want you to lead the rest of the forces, John and I are going to take Tracy. One way or another, Tracy will be dethroned." Gary and the others nodded their heads and Gary said, "Be careful, Kanto's one of the Loyal Regions to the Comet Empire, if not the Loyalist." The two nodded their heads, got in a humvee and drove towards Pallet Town. Gary then looked back at Vermillion City as the Alliance was fighting for every city block to take it. Bonnie smiled and said, "let's get to work." Gary nodded his head and said, "Send the Kalos 3rd Armored division to Cinnabar island, in case they try something."
"Got it sir." Said a soldier. Gary then said, "Let's get the Alpha Region's infantry to secure the connecting route for Kanto and Johto to cut off their forces. Then have the Bravo Region's helicopters fly over and mark sniper positions in the city." another soldier nodded his head and ran off. Bonnie smiled at him and said, "You are good at this." Gary smiled and chuckled before saying, "Yeah, but this job isn't for me permanently, I want to be like my grandpa." Bonnie smiled and said, "Professor Oak is proud of you Gary, we all are." Gary smiled back and said, "Thanks Bonnie, now let's get to work on ending this war." Bonnie agreed with him and they worked together to secure Vermillion City, the siege lasted for some time before the defenders eventually gave up and the capital of the Comet Empire was taken.
Meanwhile, after leaving their friends in command of the army, John and Ash drove through Cerulean City, Pewter City, Viridian City, until finally they reached Pallet town. Getting out of the Jeep, the two saw how much the town had changed, the buildings looked old and decayed, the grass overgrown for some houses. Walking forward a bit, John and Ash saw bodies of protestors littering a side street. John looked at Ash and he looked back at him. Tracy had gone too far. Soon they saw the vehicle Tracy used to get away from Vermillion City at Professor Oak's old lab. Walking up the stairs, they saw the state of the once prestigious lab, the ranch in whole was left forgotten and several Pokémon laid in the fields too weak to move or weren't moving at all. Ash was the first to see the door was left opened and he entered first with John covering him. They readied their guns as they slowly walked into the lab.
"Tracey Sketchit! The time has come to pay for your crimes!" Shouted Ash, an echo of his voice sounded through the nearly empty lab. Soon a Vice came back shouting, "I'm not guilty of anything!" It was Tracy's voice. John growled and shouted, "Tauros shit you're not guilty! You plunged the Pokémon world into chaos! You caused the death of hundreds of people and Pokémon!" Tracy came back with, "That's on you two! And your Alliance!" Ash retorted by saying, "The Alliance was formed to combat the Comet Empire. An Empire YOU formed Tracy! All because you wanted me to give up my dream of being a Pokémon Master! But it was thanks to that betrayal of you and the others, I was able to finally achieve that dream!"
Soon a shell of a shotgun was loaded into the barrel and Tracy fired at where Ash and John were before they ducked out of the way before he hid again. Ash hid behind a chair and asked John through telepathy, "Can't we use our Aura to find him John?" John aimed where Tracy was but saw him gone and he told Ash also through Telepathy, "I've been trying since we came in here. He must have some kind of Aura Dampening field around the building." John then dodged another shotgun blast before shooting the shotgun out of Tracy's hands and tackling tracy.
Ash stood up and saw John get kicked off Tracy and he ran into a new area of the lab. Following him in, they saw that they were in a huge missile Silo and they saw hundreds of missiles armed with the gas that they saw on Alola. That was when alarms began to sound and a recorded line say, "Missiles Primed, target, Otron Region, locked. Target, Alola Region, locked…" John and Ash looked at each other and then they saw the command center with Tracy inside it. They ran with all they could into the window and tackled Tracy again as John tried to stop the countdown as the computer kept listing targets. Ash tied Tracy up and searched for anything to help John until he found a key card. Tossing it to John, he shouted, "Try that!" John caught the card and plugged it into the computer and a password box appeared. Thinking like Tracy, John tried Comet Empire and miraculously, it worked and he shut down the missile launch.
"NO! YOU FOOLS! YOU DOOMED US ALL!" Shouted Tracy. John and Ash looked at him and Ash asked, "What do you mean?" Tracy told them, "The Gas Canisters are on a different timer, stopping the missile launches didn't stop the gas canisters from opening and allowing the gas to expand." John looked and said, "Ash get Tracy out of here, I'm gonna try and contain the gas." Ash grabbed John's arm and shouted, "I'm not going to be the one who told Shauna that you died of the gas. We are all getting out of here!" John looked at the room before they all got out and then used his Aura to seal all the cracks to make sure the gas didn't escape…
"John?!" Shouted Ash. John looked at him and said, "WE GOT TO KEEP THE GAS FROM GETTING OUT!" Ash looked at Tracy, grabbed his collar and shouted, "HOW?! WHY?!" Tracy simply chuckled and said, "cause it was to be used in your region." Ash growled and punched Tracy's lights out. John then heard the gas canisters open and he got him, Ash, and Tracy away from the door as he got ready to use water Pokémon to use water type moves to neutralize the Gas in the launching room right as Arceus came in in his Water type form and used a huge rain dance as john used his aura to reopen the missile silo doors and together, they neutralized the gas.
The next day, the news of Tracy's capture was shown on the TV and the comet Empire forces still fighting eventually all surrendered, the war was over. Now was the time of the trials of those in command of the Comet Empire. Each of the traitors and those who followed them were charged with Pokémon Abuse, the execution of prisoners, firing on civilians, illegal experimentation on humans and Pokémon, using Chemical warfare after it was banned from all wars. Those still loyal to Ash all testified against those in the comet Empire. Misty, Clemont, and Iris all testified for Ash as well and how Tracy bribed them to betray Ash and help him make Team Comet and then the Comet Empire. They testified that Tracy Ordered Chili's death as he saw him as a traitor when Chili didn't know the truth about that day.
"We knew that Tracy would not stop until we were defeated, so we had no choice but to go on the offensive once they were forced away from the Otron Region." Ash said on the stand as he looked at the traitors who were still alive and against him. Tracy sat in the middle of the defendants. The trials went on for months and all those in command spots, including Brock, Tracy, Dawn, and Barry, were the ones who were charged. The Jury found each of them guilty on the charges. Clemont and Misty were sentenced to 10 years in prison after they helped the Alliance free the Regions from the Comet Empire, others like Cress, Dawn, and Barry were given life sentences, but Brock and Tracy were given the worst punishments.
"In all my years as a judge, I have never seen such cruelty to Pokémon and Humans. But this war and what you've done before the war have shown otherwise. Brock Hartman, Tracy Sketchit, you both have been found guilty of the crimes that were laid before you. Normally you would get life sentences, but due to your parts in creating the Pyroar Virus that decimated an Island in the Alola Region, you both are sentenced to death by hanging. You will be taken to the Otron Region where you will be publicly hung in the capital until you are both dead. May you find peace in your lives after this one." said the judge before he banged his gavel and the court was adjourned. John and Ash smiled in satisfaction as Brock and Tracy were taken away. After the trails, the core Regions all cheered in celebration at being liberated after 10 long and harsh years.
_X_ 20 YEARS LATER
"And that was the whole war between the Alliance and the Comet Empire." a wiser and older Ash said to his Grandkids, Ash Junior and Delia the Second. John and Shauna both smiled as were Aubrey and Zavier after their grandpa finished the story. They smiled and Ash Junior said, "When I grow up grandpa, I wanna be just as awesome as you." Ash smiled and said, "well with your Torchic, I doubt you'd fail." Delia the Second then said, "and I wanna be a Top Coordinator like grandma." May smiled and said, "I can teach you all I know so you can be the best." their grandkids cheered and ran out of the house excited for their future Journeys.
Ash had Mat lean on him and he held her close as he thought back to what happen after the trials, Bonnie and Max dated for 3 years before Max popped the question and Bonnie said yes, Misty and Clemont were let go early for good behavior and were put on Probation for the rest of their sentences. Clemont was allowed back into the gym by Bonnie but was forbidden to partake in gym battles. Instead he focuses on helping his dad and his stepmom take care of his half brother Billy, who was told about Clemont and had a small resentful side. Grace accepted the fact that Serena was dead and moved to Lumiose city to be with her new grown family. Tierno helped the rebuilding of multiple locations and eventually moved to Unova and took over Brycen's Gym, keeping the Ice typing for the gym.
Every Gym Leader that joined the Comet Empire was forced into resigning from the Pokémon League, their Pokémon taken, and they were all hauled off to jail to spend the rest of their lives. Chili's leg healed and now he's turned the Striaton City Gym into a FIre type gym only. Iris was banned from the Dragon Village and now roams the countryside of Unova seeking purpose. Roark took over his dad's gym and left the Oreburgh City Gym in the hands of a loyal rock type trainer. Dawn was barred from entering Pokémon Contests ever again once she got out of Prison and Barry was also barred from entering the Pokémon League. In Alola, the Alolan forces used water type moves alongside Kyogre to neutralize the gas that was surrounding Akala island. Tapu Lele was brought back to the island and it slowly became its old self again. The war affected all regions involved, many people died for what they believed in. In the end of it all, the Alliance of Free Regions showed that it had what it needed to fight, beat, and defeat the Comet Empire, those who fought in the war wishing to never fight in a war like that again.