So the series would take place in the newest region. Ash is of course entering the Pokemon League. Unlike all the other anime, he doesn't have any companions. At least not any permanent ones.
First episode, Ash and Pikachu arrive, but so do Team Rocket. Team Rocket goes on about how Ash has no friends or Pokemon besides Pikachu to help him, and that the time to take Pikachu is now. They proceed to steal Pikachu, and Ash tries all he can to get him back, but fails. Team Rocket then heads back to Team Rocket's base.
Second episode, Ash becomes pretty depressed. He can't go back to Kanto because he has no way to get there. He eventually decides to just proceed with the league, so he has Oak send him a Pokemon.
Third episode, Ash uses the sent Pokemon to catch a regional Pokemon. He goes to the first gym and wins his first badge.
Ash catches two or three more Pokemon. Since Team Rocket isn't in the region at the time, a new villain will probably have to be introduced. I had an idea for one who's jokier than the trio, but also stronger. His name is Hat Thief (his real name is never revealed), and he becomes obsessed with Ash's hat, and goes to great lengths just to steal it. His starting Pokemon is a Murkrow. He wouldn't be in every episode, but he'd make frequent appearances.
Ash reunites with Gary, who he learns came to the region to do research. Gary is also able to teach new moves to some of Ash's Pokemon. Ash and Gary spend several episodes together before splitting up. Ash wins his second gym battle. After catching even more Pokemon, he returns the sent Pokemon to Oak, also sending some of his other ones. Meanwhile, Hat Thief debuts Lotad, his second Pokemon.
At the end of the first season, Team Rocket has successfully brought Pikachu to the Team Rocket base. Pikachu tries to escape, but it's no use. Giovanni proceeds to capture and work on brainwashing Pikachu. The trio heads back to the new region.
Near the start of the second season, Ash reunites with Paul, who he learns came to the region to enter the league. Paul has brought his Torterra and Electivire, and is catching new Pokemon. They quickly find the third gym, and both win. After more episodes, they find the fourth gym. Paul wins, but Ash doesn't. Paul bids Ash a fair goodbye as he heads to the next gym alone.
Ash trains. During an attack from Hat Thief, Lotad evolves (but they still lose the fight). Ash has a rematch with the fourth gym, and wins.
At this point, Ash's party is entirely different from the first full party he had. At the beginning of the third season, Team Rocket makes it back to the region, and continues to antagonize Ash. Ash is reminded of Pikachu, but just stays strong and fights with less tolerance than before.
Ash sees a miniature tournament for anyone who has earned at least four badges. It's not just a normal tournament though; matches will have special rules like Fire-types only, trainers have to use each other's Pokemon, triple battles, etc. Ash does some training and enters. About halfway through, he learns that Trip has also entered the tournament. They meet up and wish each other luck, and watch each other's battles. They are the final two, and square off in a standard battle with no special rules. Trip wins. After the battle, Trip explains that the gym he just came from is tough unless you have the right Pokemon. He generously lends Ash a Pokemon to use for the battle, and Ash promises to give it back at the Pokemon League.
Hat Thief goes into a hat store. He looks at all the hats, and deems that none of them are anywhere near as cool as Ash's. He starts to sulk, wanting Ash to just give his hat to him. The store owner comes and has a chat with Hat Thief. Understanding the situation, the store owner gives Hat Thief a Mismagius that should prove useful in stealing Ash's hat, using its Psychic. In his biggest scheme yet, Hat Thief sets up some kind of haunted house to scare and trick Ash, and take his hat. It works and Hat Thief makes his escape, but in the next episode, Ash tracks him down, defeats Mismagius, and takes back his hat.
Ash catches a couple new Pokemon, and beats the fifth gym, with Trip's Pokemon as his lead. Back in Kanto, Misty, Brock, and Tracey discover that Pikachu was captured by Team Rocket, and that Team Rocket has begun huge plans for capturing lots of Pokemon. Misty, Brock, and Tracey try to infiltrate Team Rocket's base, but are easily overpowered. They decide they need some help, so they message May and Dawn. With Oak's help, they message the other professors, who get the word out to Iris, Cilan, Serena, Clemont, Kiawe, Lillie, Mallow, Lana, Sophocles, and Gladion.
Hat Thief follows Ash as he goes through a cave to reach the next city. After squaring off, Ash knocks Hat Thief away, and runs off. As he recovers, Hat Thief finds a Dusk Stone. Soon after Ash reaches the next city, Hat Thief throws out Murkrow. He also surprises Ash with the Dusk Stone, which he uses to evolve Murkrow. Ash defeats Hat Thief in a challenging battle.
At the beginning of the fourth series, Ash reunites with Sawyer, who he learns came to the region to enter the league. Sawyer has brought his Sceptile, and is catching new Pokemon. They both win at the sixth gym.
Hat Thief and the Team Rocket trio team up in an all-out scheme to steal Ash's hat and all his Pokemon. With the help of Sawyer, Ash fends them off and gets everything back. At the seventh gym, the old gym leader is about to leave and turn responsibility over to the new gym leader. The old gym leader wants to do one more battle, but the new gym leader is eager to start and begs him to leave. When Ash and Sawyer arrive, the gym leaders get an idea to do a double battle, and that if Ash and Sawyer win, they'd both get a badge. Ash and Sawyer pull off the victory. Sawyer parts ways with Ash.
Brock, Misty, May, Dawn, Iris, Cilan, Serena, Clemont, Kiawe, Lillie, Mallow, Lana, Sophocles, and Gladion finalize a plan to get back Pikachu and stop Team Rocket once and for all. After making it past the beefy guards and high tech security systems, they reach the rooms with all the stolen Pokemon. However, they don't see Pikachu. Giovanni discovers them and appears on a screen, but heavily shaded. He is petting something. He releases all the Pokemon, which form a massive army. Brock asks where Pikachu is. Giovanni flips on a light, showing that the Pokemon isn't his Persian, but instead Ash's Pikachu! He explains that Pikachu is his star when it comes to stealing Pokemon. The stolen Pokemon all attack, leaving Ash's companions to fight for their lives.
At the beginning of the fifth and final series, Hat Thief catches a Breloom using Honchkrow. Breloom becomes a regular in Hat Thief's schemes, thanks to its Spore.
Ash arrives at the eighth gym, but the gym leader isn't there. The Pokemon League is also approaching fast. Ash can't seem to find the gym leader no matter where he goes. On the last day to sign up for the league, Ash hurries to the gym as soon as he can and challenges the leader. The battle is the hardest battle Ash has had in the region so far. Not only is it difficult, but it manages to drag on and on, pushing Ash near the cutoff time to sign up. When Ash wins, he hurries to the stadium and signs up literally at the last minute.
Before the start of the league, Hat Thief earns some money and uses it to buy a Water Stone. At the end of this episode, Hat Thief, with his Honchkrow and newly evolved Ludicolo, successfully steals Ash's hat and makes off with it.
Brock, Misty, May, Dawn, Iris, Cilan, Serena, Clemont, Kiawe, Lillie, Mallow, Lana, Sophocles, and Gladion were all defeated, captured, and separated from their Pokemon. The Pokemon are now undergoing the brainwashing process. The companions, feeling powerless to help, all share their favorite stories from when they were traveling with Ash. They decide that they have to repay the favors for what Ash did for them, so they call out to their Pokemon as loud as they can. Hearing the cries, the Pokemon resist the brainwashing, and destroy everything with their attacks. They beat down Giovanni, nab Pikachu, and free their trainers.
The Pokemon League happens to be the biggest one yet. Ash sees Paul, Trip, and Sawyer before the tournament starts. He has Oak send in Trip's Pokemon to give back to him, but before that, Oak informs Ash about the companions' attempt to rescue Pikachu. Oak says he doesn't know what happened to them after they went to Team Rocket's base. Ash is sad, but says he's gotten stronger and wants to continue on for now. He asks Oak to inform him as soon as Oak learns anything.
Officer Jennys help Ash track down Hat Thief, who is getting ready to leave the region. Ash stops him just in time and demands back his hat. Hat Thief and Ash have a full battle to decide who gets to keep the hat. Hat Thief's final team is Honchkrow, Ludicolo, Mismagius, Breloom, Smeargle, and Slowking. After Ash wins, he takes back his hat. This is Hat Thief's last appearance.
The Pokemon League then starts. Ash is using every Pokemon he's ever caught, using them all once each. He, Paul, Trip, and Sawyer pass the qualifying rounds, and get into the big tournament. Ash, when watching other matches, sees the fun everyone's having, and starts to change. He storms off and starts vigorously training with the Pokemon he's using in his next battle. All the training he does is intense, and overly straining for his Pokemon.
Ash is pit against Trip, then against Sawyer in the quarterfinals, then against Paul in the semifinals. He wins and makes it to the final round, but Trip, Sawyer, and Paul noticed how hard he was being on his Pokemon.
When Ash is moodily watching the other semifinal match, Trip and Sawyer come and try to talk to him, but Ash rejects them. Paul then comes and tries to force him to snap out of it. Ash starts to comply, but when a trainer in the match throws out a Spearow, Ash gets super emotional again, and storms off. Ash goes to Professor Oak, and tries to get an answer, but he won't answer, so Ash runs outside, throws himself into the grass, and sobs. His rivals follow him and say he should focus on the final battle, but Ash says all he cares about is Pikachu. Then, to everyone's surprise, all of Ash's companions show up with Pikachu. They call for Ash, and as soon as he sees Pikachu, he runs over. Pikachu is knocked out and terribly injured. It was the only way to stop Pikachu from hurting them.
Everybody rushes to bring Pikachu to a Pokemon Center, but all the ones they find are full with all the defeated trainers. The only option is to work on Pikachu themselves. They try everything they can, but they can barely do anything. As they all think they're sharing their last moments with Pikachu, a Nurse Joy from one of the centers comes in. She starts to say that her center has room for them now, but she sees Pikachu and asked what happened. They tell her everything. Joy lets them in on a super secret machine that Nurse Joys have developed, called the Heal All. Pikachu would be the first to use it, but it would only work if he was in a Pokeball.
The final battle of the Pokemon League is the next thing we see. Ash's opponent is a brand new character, and his first five Pokemon are Blaziken, Meowth, Latios, Lucario, and Mega Charizard X (no particular order). Ash's first five Pokemon are Charizard, Sceptile, Infernape, Krookodile, and Greninja (no particular order). After a series of extremely epic battles, Ash's opponent throws out a Pikachu, who defeats Ash's fifth Pokemon. Ash uses his own Pikachu, who is thrown out of his Pokeball. Pikachu is confused about everything that happened, but Ash tells him to go with it.
After a lot of fighting, Ash's opponent shocks (no pun intended) everybody when he pulls a Thunder Stone out of his bag. The opponent compliments Ash's Pikachu, and says his Thunder Stone is the only way he can win. His Raichu then proceeds to wail on Pikachu. For a finisher, Raichu runs in with a Volt Tackle. However, Ash tosses his Electrium Z to Pikachu, and counters the Volt Tackle with a Z-Move. Everybody in the arena is electrocuted (literally) by the massive clash. When the smoke clears, it's revealed Pikachu wins!