I don't own Pokemon or the idea of this story which I got from Captain Buggles. I just own my OCs.
TMs will exist in this universe but instead of replacing older moves I will just add to the list like TM02 is still Razor Wind but Headbutt is TM57. I will put a list of TMs in this universe on my profile and I'll just make the HMs TMs as well and I forgot to mention this earlier Ash can carry nine Pokemon on him.
Continuing their adventures in the Orange Islands, Ashley and her friends have stopped off at Mandarin Island. After recalling Lapras, the quintet hear a commotion, and notice a Grimer, Voltorb and four Magnemite attacking their Trainers. Eager to investigate, Ash and the others run to help. However, as Pikachu approaches, he stops. When Ash inquires as to what is wrong, Pikachu just glares at his master. Out of nowhere, Togepi jumps out of Misty's arms and glares at its Trainer as well. Pikachu and Togepi then join the other Pokémon, while Voltorb explodes, distracting Ash from rescuing his Pokémon. When the dust clears, Officer Jenny has arrived, but the Pokémon are gone.
At police headquarters, Jenny explains that for some time, Pokémon have all been disobeying their masters. The only Pokémon that doesn't appear to be affected by it is a Gastly. Jenny explains that she is hoping by using Gastly, they will be able to figure out what is going on. Ash and the others vow to help as well. Ashley decides to use a Ghost type that is immune to Psychic type attacks and gets Spiritomb from Professor Oak's Lab and sends back Pidgeot.
She then checked Spiritomb's data and revealed that this Spiritomb is female, has the ability Pressure, and knows Dark Pulse; Shadow Ball; Hidden Power; Psychic; Hyper Beam; Will-O-Wisp; Hypnosis; and Smokescreen.
Meanwhile, Jessie and James has arrived on the island. While Jessie and James want to go exploring, Meowth becomes angry with them, saying they have important business to do. Suddenly, Meowth pauses. When Jessie and James ask him what is wrong, he takes off. Team Rocket follows Meowth, and end up in a large room. As they get up, they notice Butch and Cassidy looking at them. Butch and Cassidy explain that they are stealing all the Pokémon on Mandarin Island for the Boss.
Jessie sends out Arbok and Lickitung, while James sends out Weezing and Victreebel. While Victreebel bites on his head, Butch snaps his fingers. A Drowzee hooked up to a machine appears. As Jessie and James question about it, the Psychic-type begins using Hypnosis, causing all four of the Rocket's Pokémon to turn against them. Butch and Cassidy explain that they have Drowzee hooked up to an antenna which strengthens and broadcasts it's hypnotic power all across Mandarin Island, which has allowed them to take control of all the Pokémon on the island. Having revealed their plan, they decide to get rid of Jessie and James and set their own Pokémon onto them.
Jessie and James are later found unconscious and taken to the Pokémon Center. When they awaken, they are with Officer Jenny, Ashley and the others. After explaining that they witnessed Butch and Cassidy with all the stolen Pokémon, Ashley tries to convince them to infiltrate their base again. Jessie and James agree to help out.
Looking through a surveillance camera, Butch and Cassidy see Jessie and James roll a large cart up to the entrance of their headquarters. It is filled with Poké Balls. Jessie and James are with Indigo and Redwood who are pretending to be Team Rocket Grunts and told the Rockets that they would like to make peace, and have brought hundreds of Pokémon for them. Butch and Cassidy are skeptical, but let the quartet in anyway. As they enter, Ashley, Misty and Tracey jump out and demand Butch and Cassidy return the Pokémon. They refuse, saying that with the help of Drowzee, the Pokémon on Mandarin Island will do whatever they want them to do. Using Drowzee, they have all the Pokémon attack the Trainers. All the electric, fire and water types combine their attacks into a super-powered blast however Gastly and Spiritomb who learned Protect protect them from it.
Suddenly, Ashley gets an idea. After Pikachu shocks her, she gets up, taunting Pikachu into launching another attack. This angers Pikachu, who tries again. Ashley keeps dodging the attacks, all while taunting Pikachu. Everybody is confused as to what Ashley is doing. As Gastly and Spiritomb start to weaken, Ashley gets in front of the machine controlling Drowzee and taunts Pikachu into giving him everything he's got. Pikachu launches a massive Thunder Shock, which strikes not only Ashley, but the machine as well. As a result, it overloads and explodes, causing Drowzee to lose control of all the Pokémon.
Misty happily runs up to Togepi, who, upon seeing her, jumps into her arms. Ashley, injured and tired, looks up to see Pikachu jump into his arms. The other Pokémon are released back onto the island, and run off to find their Trainers. However, Butch and Cassidy refuse to let Ash
Ashleyand the others leave. They challenge them to a battle, and Ashley accepts. Using Drowzee, Butch and Cassidy are able to confuse Pikachu. Then, they have the Psychic-type use Metronome. Tracey comments this is trouble, as they don't know what move it will use. At the same time, nobody notices Togepi using Metronome as well. When it completes the move, an explosion sends Butch, Cassidy and Drowzee flying, and their headquarters destroyed.
After the duo is arrested, everyone wonders where the explosion came from. Ash and friends then bid Mandarin Island farewell and head off on their next adventure.
While riding around the Orange Islands on his Lapras, Ashley finds a mysterious message in a bottle that says "If you know anything about a Pokémon called the Crystal Onix, let me know right away," which leads the gang on a new adventure. Ashley, Misty, Tracey, Indigo, and Redwood travel to Sunburst Island, which is famous for its artists and glassblowers. They meet a struggling young shopkeeper named Mateo, who's seeking inspiration from a legendary Crystal Onix. Having been unable to find this special Pokémon, Ashley and his friends decide to help him in his search.
Tracey sends out Venonat to help find the Crystal Onix. Mateo holds up the statue of the Crystal Onix his grandfather sculpted and Venonat scans the image. The group is lead to a series of rocks that are shaped like the body of an Onix. Disappointed, Tracey recalls Venonat and sends out Marill. Tracey plays Marill a recording of Onix's cry and Marill quickly detects something. Marill leads them to a body of water and points across the water to a small island with a cave. The water begins to part and a clear path to the cave is shown. They fall into a hole Team Rocket had dug to keep them away from the Crystal Onix. After reciting their motto, Team Rocket run off to find the Crystal Onix. Ashley and friends climb out of the hole and set off after them. Once they get to the opening of the cave, they discover Team Rocket got caught in their own traps. Misty refuses to help them and they all enter the cave. At the end of the cave they come across a lake. Marill dives in this lake, its tail bobbing above the surface. Marill hops out of the water and then the Crystal Onix bursts out. Team Rocket shows up, free from their traps. The two Rocket Grunts send out an Arbok and Sandslash in attempt to catch the Crystal Onix. Ashley and Misty send out Pikachu and Staryu to counterattack. Staryu and Pikachu attack Team Rocket, then the Crystal Onix smacks them in to a blast off. Mateo sends out Cloyster to battle Onix, remarking that Onix is weak to Water types. Cloyster's water attacks prove to be useless against the Crystal Onix, so Mateo sends out Charmeleon. Charmeleon uses Ember and the Crystal Onix is engulfed in flames. Mateo stares at the Crystal Onix, who returns his stares. The Onix then faints into the water. Ashley calls out at Mateo to catch it, but Mateo says he doesn't need to, he has found inspiration through the Crystal Onix. The Crystal Onix dives back into the water. Back at his shop, Mateo and Charmeleon are busy making a glass figurine. Ash and his friends wave goodbye to Mateo and Marissa. Mateo made Ash a lifelike glass sculpture of Pikachu. Redwood bought a glass sculpture of a Mr. Mime for Delia.
Aboard the two Lapras, the group follows a news crew to Fukuhara Island No. 4, where a scientific expedition is underway after the discovery of a fossilized Kabuto. While on the island Ash and the gang are shocked to find out that Nurse Joy is the director of the Kabuto excursion. While listening to Nurse Joy being interviewed by a news reporter they find out that the reason why the crew has come out to the island is to study the habitat of the extinct Pokémon Kabuto. She also remarks that they would like to find out if the claims about Kabuto oil are true or not. The claims being that the oil can not only bring good health, but also cause someone to live forever. After hearing all of this Ashley and Tracey jump in front of the reporter's camera and ask if they can help with the fossil digging.
After the Team Rocket scene the show cuts to Nurse Joy leading a group of explorers, the news crew, and Ash's group to the digging site. A group of Growlithe also accompany the team to possibly find the scent of the Kabuto. While Machoke are seen carrying some equipment, along with Rhydon for drilling holes. As they pass by, a mysterious silhouette of a man is seen behind a tree. They eventually reach a small cliff path which Misty is very uneasy about because of the height. At the same time Team Rocket is shown following the same path on a lower section of the cliff. As Nurse Joy's team moves on the Growlithe start to growl at a large boulder on a hill at which Nurse Joy dismisses. Suddenly the boulder gives way and starts racing towards them. As the boulder races down the viewer can see a leg of a man on top of the hill, hinting that the boulder was pushed down by him. While the group is running down the hill Ashley tells Nurse Joy to use the Machoke at which she agrees and tells them to stop the rock. They succeed and the team is saved. Unfortunately for Team Rocket, the boulder then rolls off the side of the cliff and hits a Rocket Grunt on the lower level of the cliff into what looks like a canyon.
As the team keeps walking once again a silhouette of a man is seen, but this time from behind a rock. Pikachu catches a glimpse and looks over which catches Ashley's attention. After not seeing anything Ashley says, "Nothing there Pikachu." and turns around. Although, the moment she turns around the man's figure can be seen again. Eventually the team reaches their destination, a hidden bay on the island's desolate northern shore. Right away the crew gets down to digging with some Machoke and Rhydon pitching in. As Ashley, Tracey, Pikachu, and Togepi dig, a bunch of boulders start falling down from the top of the cliffs onto them. Luckily Nurse Joy commands Rhydon to use Horn Drill on the crashing boulders and once again the team is saved.
After the second near boulder catastrophe Misty mentions that she thinks all these accidents aren't really accidents. That maybe someone else is causing all these bad things to happen. Tracey brings up the point that the island is supposed to be deserted and that can't possibly be true. Just as he says that a dark silhouette of a man is seen running from behind a tree at which Pikachu notices and starts chasing after him. Ashley follows suit and ends up jumping on the man bringing them both to the ground. As the rest of the crew catches up the identity of the man is finally revealed. With that he then sternly tells them all to leave the island while admitting that he has been the one who has been pushing the boulders onto them.
The man then explains that he was only trying to keep them out of danger. He then tells of an ancient prophecy which implies that anyone who comes to the island to disturb the Kabuto will cause the island to be swallowed by the sea. At that moment an explorer comes running into the forest, ecstatic to have found another Kabuto fossil. This then causes the team and the man to venture into a cave where the fossil was found. When they get to the end of the cave they find tons of Kabuto fossils on the wal. The Kabuto then end up getting revived so Misty catches one and Ash catches one and is going give it to Brock.
As the island starts to crumble apart the team decides to head for the boat, but the strange man insists that the prophecy said to run into the forest and make a raft. So they listen to the man and start building a makeshift raft. As the island sinks they all jump on the raft and Redwood sends out his Gyarados to pull the raft. They all make it to sea safely and watch the island completely sink. Joy remarks that maybe the Kabuto oil does cause them to live forever. She then apologizes to the man for not believing him and the news reporter says that she thinks it's best that no one ever find out the Kabuto's secret. At the end the Kabuto are seen swimming towards the moonlight, looking for a new safe home.
The quintet find a stage boat with hidden people using ventriloquism so it looks the Pokemon are speaking. On Kinnow Island Indigo let Misty borrow his TM98 which contains Calm Mind to help her Psyduck with his headaches and met a girl named name Marina and a wild Golduck which Marina caught.
Ashley and her friends spot Navel Island, the home of the second Orange League Gym and the Sea Ruby Badge. They touch down on the beach near a very quiet village, but the Gym is nowhere to be found. A man approaches on a sailboat, introducing himself as Danny and immediately appealing to Misty, shocking Ashley and Tracey. Tracey thinks Danny is another Trainer seeking the Gym Badge.
They approach the Navel Gym gate, and Ash opens it. Inside, there is a cable car and a trail leading up the mountain. Pikachu points at a sign that gives instructions. It declares that challengers must climb up the mountain without using Pokémon or risk disqualification, while spectators can use the cable car. Danny also climbs along, moving at a seemingly easy pace while Ashley is struggling with both the exertion and a slight fear of heights. At one point, Misty and Tracey pass via the cable car.
Ashley and Danny continue hiking up, the weather turning to snow. Ashley shivers while Danny seems unaffected. Pikachu collapses from the cold and Ashley runs to Pikachu, taking off his vest and wrapping Pikachu and holding him closer. Danny watches with admiration as Ashley and Pikachu press forward. At the summit, Misty and Tracey are waiting, wrapped in blankets. Ashley and Danny arrive, and they run to meet. Misty runs past Ashley to Danny, offering to share her blanket. Danny reveals to everyone that he is the Gym Leader since nobody was at the top when Misty and Tracey arrived.
Danny announces that the match is composed of three rounds, and two of three wins. The first test is to freeze a hot water geyser. Danny uses Nidoqueen while Ashley summons Lapras. Both Pokémon fire Ice Beam attacks at the geysers. While Lapras makes steady progress, Nidoqueen is much faster and freezes the geyser first, winning the round. Lapras manages to complete the task but winds up exhausted.
The second round is to carve the ice into a sled with three Pokémon. Ashley sends out Pikachu, Ivysaur and Flareon. Danny uses Machoke, Scyther and Nidoqueen. Danny's team uses brute force to make adequate progress. Flareon used Flamethrower to perfectly carve the sled and win the round.
The final round is to race down the mountain to the beach goal line. Danny puts Geodude, Electrode and Scyther into his sled while Ashley rides with Pikachu, Ivysaur, and Wartortle. When the light turns green, both teams race down as fast as possible while Misty and Tracey use the cable car. Danny's Scyther steers his sled while Ashley uses Ivysaur's vines to steer, although Ashley spins out of control.
They restart the race and launch when the sun comes out from behind a cloud. Both teams race down, as Misty and Tracey wait. The terrain changes from snow to rock. Ashley's sled picks up too much speed and barely misses a large rock, causing the craft to cut through trees. Danny closes in on the finish line, but Ashley soars through the sky and catches up with Danny. The landing causes Ashley's sled to shrink in size, and the lighter sled allows Ashley to pull forward and win the race, crashing into the ocean. Danny congratulates Ashley and hands her the Sea Ruby Badge. Ashley accepts it with excitement. Misty, Tracey, Redwood, and Indigo are glad that Ashley won, but Misty is also partially upset that Danny lost. Ashley and co. get back on the two Lapras and leave Navel Island.
Ashley catches a Snorlax on the Grapefruit Islands. On Murcott Island Tracy catches a Scyther while Ashley catches a Shiny Venomoth. While on Manadarin Island they observe Lorelei who defeated a Kadabra with a Cloyster, a Persian with a Dewgong, a Tauros with a Jynx, and a Charizard with a Slowbro. The quintet dealt with a big Bulbasaur in Troviopolis City on Mandarin Island South.
Getting a ferry from Trovitopolis, Ashley, Pikachu, Misty, Togepi, Redwood, Indigo, and Tracey are finally going to make it to Trovita Island, which is surrounded by whirlpools and huge spiked rocks. Ashley is determined to get his third Orange League Gym Badge. Suddenly, Pikachu spots a little girl and a Seel caught in the strong current, crying for help. Misty jumps into action by sending out Staryu and then swims down to rescue the girl. Ashley joins in by sending out Lapras and helping Misty bring the girl over to the island. Meanwhile, a young man has been watching the whole thing, and is impressed by Misty's actions.
While riding the two Lapras the rest of the way to Trovita Island, Ash and Misty ask the girl what she was doing out on the current. The girl, who introduces herself as Mahri, says that she and her Seel were just playing when the current sucked them in. Misty then tells Mahri to always be careful next time she goes swimming. As the Lapras and the ship both arrive in port, the young man, who later introduces himself as Rudy, arrives to embrace Mahri, who is revealed to be his sister, and thank Misty for rescuing her by offering plenty of flowers. Rudy hands Togepi to Ashley, and then dances with Misty. He compliments the young Water-type Pokémon Trainer on her daring rescue of Mahri, and asks if she could train the other Pokémon Trainers at his Gym. Misty and Ashley are both awestruck that Rudy is the Trovita Island Gym Leader. Ashley wastes no time in challenging Rudy. After a war of words, Rudy tells Ashley that if she wants to challenge him, she has to pass a small attack test.
The group head off to Rudy's speedboat, and Ashley must knock down all the targets in order to challenge Rudy. Ashley is successful with Pikachu on the first target, but Rudy is too preoccupied with looking at Misty instead of paying attention.
Ashley sees another target appear in front of them, and Staryu destroys it with a Water Gun, causing a tree to fall and send Team Rocket flying. Ash then has an easy time using Vileplume, Sandslash, and Pikachu to destroy the remaining targets, and eventually passes the test. As night falls, Rudy schedules the Gym battle for tomorrow, and invites Misty to join him and Mahri for dinner, leaving Indigo, Redwood, Ashley, Pikachu, and Tracey alone.
A few minutes later, Ashley is talking to Professor Oak on the telephone and exchanges Vileplume for Exeggutor. Oak wishes Ash good luck in his match with Rudy tomorrow. Tracey then butts in and shows Oak his latest Pokémon sketches, while Ashley and Pikachu sit down to eat their dinner.
Meanwhile, Rudy, Mahri, and Misty finish an exquisite dinner and head down to the Gym to see Rudy's Pokémon working out by dancing to music as a way of improving their skills. Rudy and Misty get out on the dance floor, shortly followed by Mahri and Togepi. Rudy asks Misty if she would stay with him and Mahri forever. Given food for thought by those words, Misty stops dancing to think about it, while Rudy tells her to make her decision after the match tomorrow.
Ashley decided to scan Rhydon and learned that Rhydon is male, has the ability Rock Head, and knows Take Down; Horn Attack; Double-Edge, Tail Whip; Horn Drill; Rock Slide; Earthquake; Megahorn; Drill Run; Smart Strike; Fire Punch; Thunder Punch; Ice Punch; and Mega Punch.
The next morning, Ashley and Rudy are both ready to battle each other on top of one of the island's huge spikes. The spectators, Misty, Togepi, Redwood, Indigo, Tracey, and Mahri included, watch from a hot-air balloon, and one of Rudy's friends does commentary while riding a Pidgeot. As the match begins, Ash sends out Rhydon and Rudy sends out Golem since both are Ground-type Pokémon. Rhydon defeated Golem with Smart Strike, Drill Run, and Ice Punch
Meanwhile, Mahri asks Misty what Rudy said to her last night. Misty uneasily answers that it was nothing important, but obviously, she's still thinking about the offer from Rudy.
For the next round, both Trainers will use Grass-type Pokémon, so Ashley sends out Exeggutor and Rudy sends out his Exeggutor, and asks for some music. Ashley quickly order Exeggutor to use Sludge Bomb, which is super effective then Ashley told Exeggutor to keep using Sludge Bomb and the second victory goes to Ashley.
Now, in the third and final round, Water Pokémon will be used, so Ashley sends out Wartortle, and Rudy sends out Starmie, as well as dedicating the final victory to Misty. Wartortle and Starmie both attack each other with Water Guns, and Rudy quickly plays some more music, causing Starmie to spin so much, it uses a Thunderbolt attack to knock Wartortle into submission, leaving Ashley horrified. After thinking over the chance of a lifetime from Rudy, Misty finally makes her choice: She decides to go out with Rudy but she wants to travel more first she yells at Ashley to win since she can release Wartortle's hidden power Mahri is shocked, while Rudy loses his concentration after hearing Misty's words. Ashley tells Wartortle to fight back. Wartortle escapes the Thunderbolt and uses his newly learned Hidden Power, Withdraws inside his shell as it's about to fall off the cliff, then releases huge jets of water from its shell to fly back onto the battlefield. Wartortle uses Tail Whip and Skull Bash to defeat Starmie, giving the final victory to Ashley, who celebrates by dancing with Wartortle and Pikachu about how they need one more Badge to get into the Orange League. Misty and Rudy exchange numbers.
As the sun sets, Ashley receives his Spike Shell Badge from Rudy, who also offers Misty one more bunch of flowers. And so, Ashley, Misty, Tracey, Pikachu, and Togepi board Lapras while Redwood and Indigo ride on Redwood's Lapras and sail off into the sunset.