Paul was in Poni Island, where the Hoenn and Sinnoh Champions, Alyssa, and Ash were located. Team Plasma were giving refuge to Team Rocket in Alola and Paul's secret mission was to apprehend Ash and Alyssa. Paul was with Dawn and the Kanto-Johto Champion, Misty recommended Dawn and Brock along with Infernape accompany him much to his annoyance for Dawn accompanying him as he wanted to keep Dawn safe. He was here, having a battle with Ash who was surprisingly ruthless. Dawn wore her cheerleader dress and was cheering Paul and Brock was also cheering Paul.
"Infernape, dodge!"
"Electivire, Thunder!"
Infernape dodged Electivire and Electivire used Thunder on itself to make itself stronger. Electivire then rapidly went after Infernape and then held Infernape with it's tail and use Thunder. Paul smirked, he knew that Infernape's Blaze ability would be unleashed. As for Ash, his memories suggested he was doing a very wrong move but he did not know why his memories suggested that to himas he never remembered battling Paul. Alyssa was panicking as to whether Ash woud remember his memories.
"Flare Blitz!"
Infernape then used a powerful Flare Blitz and then Electivire continued to use Thunder but Infernape's attack was more powerful and then Electivire lost health and fainted. Ash felt a vague remembrance of him doing a wrong move but he did not know why.
"Apprehend Ash and Alyssa!"
Ash and Alyssa were soon apprehended and Ash felt like he was remembering something from that battle. Alyssa was then taken separately from Ash and the two were placed in two helicopters to take them back to Kanto-Johto. As for Poni Island, it fell under the control of Kanto-Johto and was the fitrst Alolan island to fall under the Kanto-Johto authority.
"Paul, we won! I do not know why Ash does not recognise us but maybe he does not recollect." Dawn smiled and said.
"Yes, Paul, you were amazing. You were in charge of annexing Poni Island and you did that." Brock said.
"Thank You." Paul said.
Paul, Dawn, and Brock then went and sat in their aeroplane. The aeroplane soon took off and was flying in the sky. As for Ash, he was very disappointed that him and Alyssa, two top Team Rocket agents, were apprehended and that he was separate from Alyssa. The villianous teams in the world controlled the other regions apart from Kanto-Johto and Team Rocket had the assistance of Team Plasma in becoming again a feared team. But now, the main Team Rocket base in Poni Island was destroyed and the Team Rocket members were arrested.
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Ash was in front of the person whom he considered his enemy, Misty, and the bane of Team Rocket. Misty was said to be the person who went affter Team Rocket and brought them down before and again, now as Team Rocket bases in Hoenn and Sinnoh were being dismantled. To his happiness though, Giovanni and his elite guard were able to escape, as he learned from his phone.
"Ash, you have done the crime of aiding and abetting Team Rocket in Sinnoh! You are being investigated as to what crimes you have commited." Ash laughed on hearing what Misty said.
"I did all the things legally according to Sinnoh's laws and systematically removed them. You will apply Kanto-Johto's laws retroactively?" Misty knew that what Ash said made sense.
"You have come under the legal sysem of Kanto-Johto and to your information, Hoenn and Sinnoh is close to falling under Kanto-Johto control. You have done what are considered crimes to Kanto-Johto." Misty said.
"Yes, so, you will make me to be in the jail till I die? I have no problem, Giovanni will come to save me." Ash said.
"We will bring Giovanni to justice. He is just a running criminal boss with soon to have almost no power as Hoenn and Sinnoh will soon fall under our control." Misty said and Ash smiled.
"I know that you have attempted to destroy Team Rocket but we will survive." Ash said.
"Could you tell me about the two times?" Misty asked as she was curious.
"Once, you and Mewtwo destroyed Team Rocket bases one by one, then you approached Giovanni to kill him but Alyssa was able to defeat you as G-Men help arrived too late and Team Rocket was able to suceed. Now, you are attempting to destroy Team Rocket." Ash said.
"Our records suggest that you were the one who were trying to destroy Team Rocket once and you failed. Then your memories were changed." Misty said.
"I always remember that I am a Team Rocket member!" Ash said.
"Yes, you were, and this is a long story..." Misty then narrated the long story to Ash.
"I do not believe you. You are replacing your role with me!" Ash said.
"So you are saying that I and Brock traveled in Kanto then Brock left me and Tracey traveled with me, and then Tracey reached Professor Oak and then Brock traveled with me in Johto, Brock, May, and Max traveled with me in Hoenn and Kanto, and Brock and Dawn traveled with me in Sinnoh?" Misty asked.
"Then you were kidnapped and made to be a Team Rocket member but somehow you escaped and made it your mission to defeat Team Rocket. Then you were again made to join us by making you have different memories but you were taken from Team Rocket and you realized that Team Rocket were bad and tried to destroy them with Mewtwo only to fail." Ash said and Misty laughed.
"I am sorry but that is your story. The reality is that is your story." Misty then showed a video showing him his battle with Paul.
"This video is fake!" Ash shouted.
"There are many witnesses to this." Misty said.
"You are forcing them to say what you want to make me to go against Team Rocket." Ash said.
"You speak with them." Misty then went and left the room where Ash was in.
"Dawn, you go and speak with him." Misty said. Dawn then went and entered the room where Ash was in.
"You will try to convince me that I travelled with you when the fact is that Misty and you, Dawn, traveled along with Brock." Ash said.
"Ash, I traveled with you throughout the Sinnoh region and that is the truth. I never traveled with Misty." Dawn said.
"Now that I think about it, I think I saw you once before and I also feel like battled with Paul." Ash said and Dawn smiled.
"Tell me when you battled with Paul!" Dawn said and Ash suddenly felt that he remembered what Dawn said.
"I feel like I battled with Paul in Lake Acuity once with my Pokemons, although I do not recollect the Pokemons." Ash said.
"Why?" Dawn asked.
"That is because I had a rotating team and had different Pokemons and I battled with many trainers on that day." Ash said and Dawn sighed. At least, Ash felt like he battled Paul. Dawn then went and left the room and then saw Misty.
"Misty, Ash remembers Lake Acuity battle with Paul! We need to send Paul!" Dawn said.
"Paul, you have an important duty. You go and speak with Ash on his battle in Lake Acuity." Paul nodded to Misty. Paul then went and reached the door. Paul then opened the door and walked to reach Ash.
"Ash, I will tell you about the battle we had. I and you battled and our last Pokemons were Monferno and Electabuzz. I defeated you on that day. Here is Infernape." Paul then released Infernape out of the Pokeball.
"I traveled with you in Team Rocket but you abandoned me one day which is fine." Infernape nodded to what Ash said.
"Did you know that I released Infernape as a Chimchar?" Paul said.
"Oh, that is interesting." Ash said.
"To whom did you think that Infernape went?" Paul asked.
"To Misty?" Ash asked.
"How did you get Monferno who battled you?" Paul asked.
"My Chimchar evolved to Monferno who battled you." Ash said.
"Is this the same Infernape?" Paul asked.
"Yes?" Ash answered.
"What happened to Misty's Infernape then?" Paul asked.
"She still has Infernape." Ash said. Paul then went, switched on the television, and showed Ash a video of the battle with him. Innfernape was also watching the battle.
"Why does the Infernape in the television resemble my Infernape?" Paul asked. Ash was thinking deeply, if Misty was correct, that would be Paul's Infernape which left him after he joined Team Rocket, but if he, Ash, was correct, that would be Misty's Infernape which would still be with her but maybe Paul has Misty's Infernape which left her when she joined Team Rocket which made no sense to him as he said that was his Infernape.
"Maybe it is Misty's Infernape which left her before when she joined Team Rocket." Ash answered which he did not believe much in.
"Then when Misty wants to destroy Team Rocket, why is Infernape not with her? You also told that was your Infernape." Paul spoke.
"Maybe he has more of a bond with you?" Ash answered but knew his answers made little sense.
"What happened to your and Misty's Infernapes? Make a coherent answer." Paul demanded and again Ash was deep in thought. Ash knew that the Infernape in front of him had a bond with Paul but he had no idea as to what happened to his Infernape. Infernape was also acting like it belonged to him by smiling at him. Misty then opened the door and then went and sat on the bed. Ash noticed that Infernape seemed closer to him and Paul which meant something he did not want to believe that Paul had his Infernape as that would make Misty correct. But if he was correct, Infernape should be closer to Misty and Paul.
"The TV Infernape could be an altered video and I know it resembles the Infernape in front of me. I remember Infernape abandoning me and Infernape could have abandoned Misty when she joined Team Rocket but Infernape is closer to me and you, Paul. The Infernape is mine then? Then Misty could still have her Infernape but we at Team Rocket know about all her Pokemon but we just know than it belongs to her." Ash said and Paul and Misty nodded.
"Why did Infernape abandon you suddenly?" Paul asked and Ash was thinking for some time and had no answers. He again thought the Infernape belonged to Misty but that made little sense. Maybe Paul caught an Infernape. Maybe Infernape was just acting but Infernape seemed to really be closer to Ash and Paul than to Misty.
"I have no idea! Maybe my memories were altered just like Misty's were. If Misty's memories were supposed to be altered, maybe my memories were also altered!" Ash said as that was also possible.
"Ash, I never had an Infernape." Misty said with full conviction.
"I need to think it over." Ash said and Misty and Paul nodded. Misty and Paul then left the room with Infernape also leaving the room while looking at Ash.
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Alyssa looked at the walls of the jail for some time and then noticed that Misty opened the door. Misty then looked at Alyssa, straight in the eyes, and Alyssa knew that she would say something serious. Alyssa saw as Misty sat on a chair opposite to her.
"Why did you brainwash Ash?" Misty asked.
"Yes, we in Team Rocket did that! That is how we were able to have relevance." Alyssa smiled and answered.
"Why did you betray us all by supporting Giovanni and making Ash to support Team Rocket?" Misty asked.
"My alleigance is to Team Rocket, so even if Ash did not support Team Rocket, I made him to support Team Rocket! Now me and my lover boy are united in supporting Team Rocket!" Alyssa answered.
"Giovanni would just be a running convict, I will make sure to destroy his empire and make it mine, after he took my love from me! Also, know that I have Mewtwo as my Pokemon." Misty said.
"I will be taken away before you have me killed in your kangaroo courts." Alyssa said.
"Yes, you will just be a running convict along with Giovanni. We will make sure that Ash returns to opposing Team Rocket and then you will have to face Ash." Misty said.
"By the way, how did you catch Mewtwo?" Alyssa asked.
"Yes, how I caught..." Misty said.
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Mewtwo saw the result of the fight between Ash and Giovanni with Giovanni winning and rapidly teleporting away with Ash and Alyssa. Mewtwo then rapidly teleported away from the area, flew to Cerulean City, and saw Misty, who was close to Ash. Mewtwo then flew to Misty to report to her the news.
"Apologies, Ash has been captured by Team Rocket due to Giovanni and Alyssa." Mewtwo said.
"That is very disappointing." Misty said.
"It indeed is." Mewtwo replied. Misty was then looking at the river and thinking for some time. Then she thought about a radical idea.
"Mewtwo, can we join forces and defeat Team Rocket? Team Rocket took my love and your first human friend. I wish to destroy Team Rocket. Will you help me?" Misty said.
"Yes, we can. I would like to be your Pokemon." Mewtwo said.
"Are you sure?" Misty asked.
"Yes." Mewtwo said. Misty then threw a Pokeball and then Mewtwo was caught in the Pokeball.
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"So easily. I am surprised by that. I will say you seem terrifiying but we in Team Rocket will prevail." Alyssa said.
"Surely we are winning. You and your group of criminals would lose to me." Misty said.
"You have a god complex. You are barely anything if Team Rocket manages to get it's hands on Legenday Pokemons like Arceus." Alyssa said.
"So you want Legendary Pokemons like Arceus? You are going to be crushed soon and those are daydreams. My Pokemons are almost as strong as Mewtwo and we could defeat whatever you throw." Misty said. Alyssa then realized that they were dealing with a powerful threat. Misty then left the room while Alyssa was looking at the walls.
Misty then heard explosions and then ran and left Alyssa's room. Misty ran and soon entered Ash's room. Misty then ran and held Ash's body and soon saw a blast and the walls broke to see Team Rocket members who were there to save Ash and Alyssa. Misty then saw Team Rocket members who ran to her and saw Ash with her.
"Starmie, go! Psychic!"
Starmie then used Psychic and threw the Team Rocket members out. The Team Rocket members escaped after losing to Paul but took Alyssa along with them. Misty then placed Ash on the bed where Ash contined to lay on the bed for some time.
"We have an injection. That will make you to regain your old memories back. If you wish no, I will not use that." Misty said.
"You put the injection as I am fine with that." Ash said.
"Fine then." Misty said.
Misty then ran and left the room. Misty soon reached the hospital ward and then she exclaimed "Come with the injection!". The nurses then ran with her and then they reached the door. Misty then opened the door and then they went inside the room. Ash lay for the injection to be applied and saw Misty and Paul wattching him along with Dawn. Ash saw the nurse take the injection and applied the injection to him and he soon was feeling sleepy and then Ash slept..
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Ash saw a black room where he saw the memories of his various journeys, he saw what Alyssa did for him. Ash then saw that flashback of him before the capture.
"Mewtwo flew away! Oh, we were so close! Let's go to the boss room." Alakazam then teleported Giovanni, Alyssa, and Ash back to the boss room where there was an injection. Alyssa used her hands to hold him and then Giovanni walked to the injection.
"Goodbye Ash, hello, Team Rocket Ash!" Giovanni then applied the injection and Ash felt the prick, shouted and then slept.
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Misty was watching the news, she saw that Kanto-Johto was able to capture Hoenn and Sinnoh. Melemele Island, the island with the largest population in Alola had a major Team Plasma base in Hau'oli City which was bombed by her forces while the city was slowly falling under the control of Kanto-Johto. Ghetsis had declared mobilization in Unova and Alola in response. Paul then opened the door.
"Ash has regained his memories!" Paul said.
Misty then rushed and left her room. She then ran in the corridor and then reached Ash's room. Misty then opened the door and saw Ash who smiled at her. Misty then rushed to be at the side of Ash and she sat next to Ash who then got up to look at her.
"Misty, you will be remembered as the leader who brought freedom to the world. You have a very strong Legendary Pokemon with you. You are truly amazing, Misty!" Ash smiled and said.
"Ash is right, Misty! I am happy to have met you as you have done a lot. Ash, will now make an announcement to Sinnoh, right?" Dawn asked.
"Yes, I will do that right away." Ash said.
"Fine, I will make the announcement." Ash said.
"Follow me!" Misty said.
Ash then followed Misty and left his room. Ash and Misty walked for some time to reach the broadcast room. Ash then entered the broadcast room along with Misty and then Ash went and stood, ready for his message to be broadcasted to Sinnoh. Misty then switched on the systems.
"I am Ash, the Sinnoh Champion, I urge all to stop the fighting in Sinnoh. I was made by Team Rocket, Alyssa and Giovanni in particular to forget my memories and support them. I have now regained my memories. I declare all Team Rocket Sinnoh members to face justice. I am sorry to what I have done but I have done them in a bad mental condition. With this, I say that Sinnoh falls under Kanto-Johto." Ash said. Misty then cut the broadcast.
"Misty, I love you a lot!" Ash said.
"Ash, I also love you a lot!" Misty said.
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Days passed and Ash and Misty were in Mount Silver, where Giovanni was last reported to have been seen. Ash insisted that he would take care of Giovanni and Alyssa, so he would go and destroy them. Misty meanwhile had done her task of destroying Team Rocket bases with Mewtwo. Bases were destroyed by Misty and Mewtwo. Agents of Team Rocket were quickly dealt with by Misty and Mewtwo and they would soon deal with the last bastion of Team Rocket members who were with Giovanni.
"Exterminate the Elite Guard of Team Rocket as they escape this cave. I am going inside." Ash said.
"Yes, I will do that, Ash." Misty said and released Mewtwo.
Ash then entered the Team Rocket base and he released Espeon to be with him. He quickly defeated the two guards who had powerful Pokemons with Espeon and Espeon used Psychic to throw them outside.
Misty then used a gun that she had and then she was thinking as this would be the first human life she would kill by her hands and not due to Mewtwo's powers. She then saw them approach her. Misty then shot the two guards in the head, making them die.
"It is good that you killed those scums." Mewtwo said.
"Thanks!" Misty said. Mewtwo then threw the bodies of the two guards off the cliff by using Psychic.