Even though it's training, Ash kind of needs it. Sadly the other things he did during this time period in the anime are not happening. Also there is an important change to the ending of chapter 3, so re-read that chapter if you wish to not be confused.
(Chapter 5: Rivalry Flares)
The police had arrested Cassidy and Barney, I mean Butch. Soon, life in Pallet Town returned to the norm, at least it tried to.
After that day, the rivalry between Ash and Gary had lengthened to very loud levels. The normally peaceful town of Pallet Town wad now full of noise, especially near Oaks lab. Thankfully, it was limited to daytime so nobody complained.
Ash quickly got himself together and trained his Pokemon hard, after seeing Gary get ahead of him, he and his Pokemon steeled themselves to training.
The normally kind and goofy trainer became temporarily strict and unforgiving. His Pokemon didn't mind much, as Ash returned to his normal self after the training. Charizard was the only one who didn't believe in their trainers methods.
Each day, Brock and Misty helped and supported him, watching the boy get stronger.
Venusaur had improved a lot, with the help of learning Sunny Day and Synthesis. He and Ash trained to calm themselves together in the sun during noon, and eventually Venusaur learned Synthesis and that quickly led him to learn Sunny Day through his normal training. His aim improved as well, the training proving itself on multiple occasions, as he broke up many fights at the ranch with carefully aimed attacks and soothing words. He also had Muk help him with sludge bomb, as the hunk was a natural at it… for obvious reasons. After a few days, he was also able to supplement his new size's lack of speed with increased bulk, with training to withstand damage instead of dodging it.
Squirtle was also pumped up and ready to train. Over the many days of training, he began to develop more and more endurance from swimming and running. He spent time perfecting his moves with target practice, and with the help of Tauros, he practiced how to aim at moving targets with more accuracy. With Ash's directions, Squirtle spent time dodging in its shell with Rapid Spin as he was blind while using the move due to being inside his shell. This quickly led to him learning Hydro Pump.
Ash asked Misty to help him train Krabby, as unlike Squirtle, it had very little training and had trouble swimming, usually just walking across the seabed. Misty was grateful that Ash actually asked her and got straight to work on training Krabby. She began with Krabby's water fighting capabilities at the beach in Pallet Town, teaching it how water can control a battle and how to ride or resist waves and currents. She also spent time teaching it attacks to control the water and gave it training on how to battle underwater. Ash trained Krabby on the land, spending time strengthening its power and endurance. He also realized he could use Krabbys powerful pincers to combat most grass type attacks, so he had grass types use vine whip and razor leaf for him to cut in battle. After many hours of training, Krabby could easily slice depart grass type attacks aimed for him.
Haunter didn't want to train as much as the others did, but Ash found a way to train him. He designated certain times of the day as times that Haunter could scare and prank any of Ash's Pokemon (except Charizard), not telling his other Pokemon, besides that it wasn't during the nighttime. Quickly, his other Pokemon developed enhanced alertness and attentiveness while Haunter developed his abilities as a ghost type better. Ash also somehow managed to explain the rules of the Indigo league to Haunter and they agreed that it would behave during the tournament, as neither wanted to be disqualified.
Ash and his Pokemon would race with his Tauros in the morning everyday, and after some discussion, one of the Tauros, the leader, was designated as the battler, while the rest just lived on the ranch in peace. Tauros trained in the fields, smashing rocks with its horns and sparring with the other Tauros.
Ash began to train Muk in a different way. Unlike his other Pokemon, Muk trained daily to take hits and hit back harder. He was showered with attacks in moderation and practiced handling it with its impressive bulk. It also began training in attacking with its arms, rather than just using sludge. Eventually, with the help of Pikachu, it learned Thunder Punch, which developed into the ability to use the other 2 elemental punches.
Out of everyone, Pikachu trained the hardest. He and Ash did everything together, strengthening their bond as they trained together, ate together and taught together. The more inseparable they became, the stronger they got. Pikachu trained mainly in the movement of his electric attacks, first trying to turn a Thundershock attack via electric control, then eventually being able to control Thunder. This also led to Pikachu learning Thunder Wave. During morning runs, Pikachu would speed ahead of the group with superior speed, making Quick Attack and Agility stronger and after accidentally smashing into a rock, he broke it revealing that he had learned Double-Edge.
Charizard mainly lazed around and didn't listen to Ash at all, he would however challenge any strong opponent he could battle against in the ranch, leading to powerful fights that Squirtle and Venusaur would have to clean up. At least he was training…
Pidgeotto and Fearow were never together, but their training was very similar. Both trained with Ash for aerial maneuvers to take advantage of their flight. Pidgeotto focused on sheer speed and her training blasted her across the ranch with power. Fearow focused on trickier spins with Ash so they could bond. Ash quickly helped Fearow learn Drill Run and Drill Peck, giving it better abilities in flight and a niche against rock type Pokemon.
…
It was 3 days before the Pokemon league. Ash walked back into his house, Pikachu on his shoulder and Haunter floating behind him. He walked into the house and saw a unfamiliar figure talking to his mother. The figure suddenly snapped his fingers, and he teleported away. Ash was initially concerned, but after looking at his mother's happy face, he realized that must have been the father she was talking about. Now was the time to talk about that.
Ash walked into the kitchen and said, "Mom, who was that just now?"
Delia turned around to see Ash and replied with, "Oh, you saw him? That's your new father."
Ash asked, "What just happened? He just snapped his fingers and left."
Delia responded, "Ah, he comes from Saffron City."
Ash sighed and dropped the big question, "Is he like Red? Will he leave us too?"
Ash never liked his father that much. The few memories that he had about him were happy, but there were too few. It was worse when 3 years before, he died on Mount Silver. Nobody saw what happened, all they found was a frozen body.
Delia knew that Ash would ask this, kids tend to like having 2 live parents. "He's training to become a part of the Elite 4, but since he trains Psychic Pokemon and can teleport to well known places, he will be around quite often. I know you rarely ever saw Red dear, but your new father will be around more.
Ash sighed, "Hopefully he is, it would be nice to have a father again."
The room fell silent.
Delia piped up, "Anyways dinner is ready!"
Ash and his Pokemon are their dinner in peace, sometimes his Pokemon would talk amongst each other.
After dinner, Ash asked his mom another question. "Is he going to watch me at the Indigo Plateau?"
Delia smiled, "We both will, so make us proud Ashie."
Ash smiled, "Thanks mom, I'm leaving tomorrow to go to Victory Road."
Delia replied, "Alright honey, I thought you would be leaving so I packed your bag with everything you need. Now have a good trip and don't forget to change your you know wha-"
"Okay mom I get it, now can I go get some sleep now?" Ash said as he climbed the stairs to his room.
Delia watched son leave the room and thought to herself, "My little boy… all grown up"
(Meanwhile...)
Jessie, James and Meowth shook as they walked towards their bosses office. They had no idea why he called them. All they knew was that they were in trouble.
They walked into the room. It was a small office at the main Team Rocket Base, guarded by several grunts and Giovanni's precious Persian.
Giovanni noticed their entrance looked at the trio calmly and he told them, "Sit down you three, we have some things to discuss… one of those being an explanation of how the authorities know the Viridian City Gym is run by Team Rocket."
The trio gulped.
Jessie took initiative and spoke up, "Uh… Well we might have attempted to steal a challengers Pokemon…"
James nodded, "Yeah, and uh he got help from some others…"
Giovanni sighed, "Well, thanks to you three, we lost one of the most important assets Team Rocket owns."
The trio gulped again.
Giovanni continued, "I've decided to give you one more chance to redeem yourselves. I will have no mercy, if you fail."
Meowth shakily asked, "What do you want us to do boss?"
"You and some other grunts…
…
Will invade the Indigo league and steal every powerful Pokemon there."
The trio looked at Giovanni as if he was insane, but quickly regained composure and saluted.
"Yes sir!"
Giovanni frowned, "You better not fail."
Jessie, James and Meowth left the room sweating.
Jessie was the first to speak up, "How are we going to be able to take all the league Pokemon? It's impossible!"
James sadly replied, "Yeah, It's the end for us.
Meowth replied to the two Rockets with a Fury Swipes Attack.
"What the hell Meowth?"
"Ow.. my face…"
Meowth yelled at the Rockets, "If this is our last stand, then we need a plan and more Pokemon. We have no choice from this, we can't run from this, so we take this to our end."
The others agreed.
"We are dangerous members of Team Rocket,we will succeed"
"I know where to get a few new Pokemon…"
Meowth nodded, "I already have a plan cooked up."
The three Rockets left in search for what they needed.
That night, James somehow managed to sneak into his childhood manors doghouse to retrieve his pet Growlithe, Growlie. When he entered, he quickly grabbed Growlie's Pokeball and after finding and apologizing to Growlie, returned him and turned to leave until he saw another Pokeball on the expensive tabletop. The Pokeball was wrapped up with a very large red bow. Shrugging, James picked up the Pokeball and opened it.
A Vulpix emerged from the Pokeball. One look at James and it glomped him. Then Growlie came out of his ball and accidentally knocked James down. The two fire types began to play around each other.
James sighed, "Well, that could have gone better…"
He returned the two fire types and left the manor. While walking back to a rendezvous point that the three Rockets had set up, James noticed something lurking in the ocean beside him. The beach he was walking on was eerily quiet, usually during the night, there would be Krabby everywhere. But something was amiss.
James turned to look at the sea when a giant wave formed. He shrieked and ran for his life until he saw what caused the wave. A Gyarados. One that was heading for him right now. James watched as it slowed to look at him.
Then the wave hit James. Suddenly instead of eating James, Gyarados grabbed James out of the water and let James ride him.
James came to a realization and pulled out a golden Pokeball from his pocket.
With a smile he said, "I'm sorry about last time, but you heard that last bit and remembered, that's what matters. Gyarados return!"
As Gyarados entered the ball, James remembered the last time he saw Gyarados, it was aboard the raft he was on, after the St. Anne incident.
(Flashback)
"Jessie, this Magikarp kinda saved us, I mean it did bring us up to the surface didn't it?"
"NONSENSE, THAT FISH IS UTTERLY USELESS"
(Jessie kicks Magikarp into the water)
"MAGIKARP NOOO!"
(A white light appears)
"GYARADOS!"
"What? But how?"
"Hello, I am James, I am your trainer!"
(Gyarados looks at James, but then leers at Jessie)
(It launches a Dragon Rage in fury)
(Everyone gets blasted off)
(Flashback end)
(Yes, this event has been changed. James is quite kind to his Pokemon in later seasons, so I believe that this would have been a more logical outcome.)
Jessie had spent a lot of her time training Arbok and Lickitung. She also had to scout out the Indigo Plateau for the plan to take action. Donning a tourist disguise she traveled to the Indigo Plateau.
While scouting the Indigo Plateau, a man in a red suit came up to her. Not wanting to look suspicious, she acted out her role.
The man greeted her, "Hello ma'am, are you here to visit the Indigo Plateau as well?"
Jessie, not wanting to be rude, replied, "Uh… Yeah, what about you?"
The man replied, "Actually I came here to scout a location for the Kanto Grand Festival. Ah, I've never introduced myself, my name is Mr. Contesta. I run contests in the Hoenn and Sinnoh region and we're thinking about introducing them into the Kanto region."
"Contest's, what are those?"
Meowth was busy working night after night. Besides James sometimes, he was the mechanic of the group and held up that responsibility well. He used the small amount of money he received to build mechs, planes and weapons as they needed them.
However one night, he noticed another shop nearby. It was a new move reminder shop in the area. Seeing this, Meowth had an idea to make up for his lack of money.
The next day, he entered the shop with a sign attached to his tail and a Heart Scale he bought. The sign read "I sent my Meowth to learn Pay Day. He can walk back to me when he is done."
The shopkeeper saw this and took the Heart Scale. After some training that nobody can describe, Meowth had learned Pay Day and could get back to work.
Meowth left in glee, "Soon, all the Pokemon in the Indigo League will be in the hands of Team Rocket! … hopefully…."
Wow look at Team Rocket, people really work hard when lives are on the line. Anyways, next chapter continues to deviate from the anime, going to Victory Road.