This season covers the Hoenn Region where the protagonist Ash Ketchum went on to further adventures and meets new friends along the way to the Hoenn League. Misty and Brock leave Ash's side. Ash meets a new friend named May, who participates in contests, and her brother Max. Brock returns and the four travel together through the Hoenn region.
Finally in Littleroot Town, Ash and Professor Birch discover that Pikachu has an electrical overload. The excess electricity causes Pikachu to run off in pain, followed by Ash and Professor Birch. Soon, a pack of Poochyena appear and chase Professor Birch, interfering with the beginning of a new journey for a young trainer named May, who after all the trouble chooses a Torchic for her first Pokémon.
Ash and May encounter a set of ruins, where they help Professor Aldon rediscover a nearly-extinct Pokémon. There, they learn about Team Magma and Team Aqua.
Ash and May have finally arrived in Petalburg City, where he hopes to battle in his first Hoenn Gym match. Ash meets May's younger brother, Max. Norman, May's father, is the Petalburg Gym Leader and Ash challenges him to a Gym battle but since Ash does not have three Pokémon with him, they only have a formal trainer battle.
Ash, May, and Max are strolling through the Petalburg forest on hopes of seeing new Pokémon and adventures. May suggest that they should stop for a quick lunch break but Max on the otherhand think that they should continue to find Pokémon in the forest. May and Max begin to pull Ash back and forth to see what he should do: eat lunch, or find new Pokémon, Ash on the otherhand get extremely annoyed and decides that they can take a quick lunch break and later find Pokémon. Ash, Max, May, and Pikachu start to have a lunch but soon find out that none of them have food on them to eat, and all of Pikachu's Pokémon food container was empty leaving them at a starving situation. Ash then tells May and Max about his friend Brock and how he always cooks meals for him. While in the forest a flock of vicious Taillow begin to attack Ash and his friends but when all hope is lost an old friend comes to the rescue.
Brock is ready to travel again and has joined up with Ash, May, and Max as the journey on towards Rustboro City. In the forest they encounter a giant Zigzagoon, which they soon realize is actually a trainer in a Zigzagoon suit. Nicolai the Knickerbocker is a trainer that believes in becoming one with Pokémon in order to understand them. While battling, he wears a costume of whichever Pokémon he is using. When not dressed as a Pokémon, he wears knickers in order to be closer to nature. Nicolai is very excited to learn that May is the daughter of the Petalburg Gym leader. He challenges her to a battle and quickly defeats her. Nicolai taunts her for losing, saying that he does not think her father will be difficult to beat since she is such an inexperienced trainer. Brock, Ash and May shrug off the defeat and continue on their way, but Max is furious. Without telling anyone, he goes off in search of Nicholai to defend his father’s honor.
Team Rocket encounters a poacher who hunts for poison-type Pokémon. When Team Rocket learn that the captured Pokémon include Koffings and Ekans, they decide to free them from the poachers grasp and they release Arbok and Weezing to protect the Ekans and the Koffings. At the end, James gets himself a new Pokémon, Cacnea.
Deep in the woods, Ash spies a Treecko. He's wanted to catch a Treecko since he first saw one at Professor Birch's laboratory. He follows the Treecko to an enormous tree that seems to be dying. There, Ash's Treecko has an argument with all of the other Treecko. It seems that Ash's Treecko is very attached to the tree and wants to stay with it, while the rest of the clan wants to move on to a new tree. Ash watches as the lone Treecko struggles to save the tree. He and Pikachu feel badly for the Treecko and try to help. In the end, however, the tree dies. Now that its home is gone, Treecko is ready to make a new home with Ash. He and Pikachu battle, and Ash catches his Treecko!
Ash's newly caught Treecko may be a bit standoff-ish, but the little green Pokémon is quite a fighter. When Team Rocket sees Treecko knocked down and hurt by a Seviper, they decide that they must have that Seviper. Meowth is very impressed with its "sneaky, snakey ways." Meanwhile, Treecko escapes from the Pokémon Center where Ash brought it to recover. When the gang finds Treecko, it is practicing its attack moves. Again and again, Treecko jumps from the top of a waterfall and tries to break a rock at the bottom with its tail. Ash is very impressed with the rigor of its training. All of Treecko's hard work appears to have paid off – when Team Rocket attacks and catches Pikachu with the help of their new Seviper, Treecko is able to save the day.
Ash, May, Brock and Max have arrived at a small city on their way to Rustboro City. Brock decides to stock up on supplies, while Max is eager to go hunting for city dwelling Pokémon. Max soon stumbles upon a very frightened Shroomish who is hiding in an alleyway. Ash, Max, Pikachu and their new Shroomish friend head off to find a Pokémon Center. On their way they pass by a deserted mansion that is being torn down. There, the gang learns that not long ago most of the city was forest and that many, many Shroomish lived in the area. They also learn that strange things are going on at the mansion, and many people believe that it's haunted. A little investigation reveals that the mansion is actually inhabited by all of the Shroomish who used to live in the forest. When the forest was destroyed, they had nowhere else to go. All of the strange noises and smells that the construction workers were hearing were actually the Shroomish! The grandson of the owner decides to tear down the mansion as planned, but to convert all of that land into a forest for the Shroomish.
On the route to Rustboro City, Ash and the gang pass by an unofficial gym boasting the world's most powerful Pokémon. Even though he can't win a badge there, Ash is intrigued and decides to battle the trainer named Anthony and this mysterious Pokémon. The world's most powerful Pokémon turns out to be a Pelipper. Pelipper attacks Ash's Treecko with a Vine Whip. It then attacks Taillow with Flamethrower. Finally, it attacks Pikachu with a Thunder Attack. Ash and crew are amazed – Pelipper should only have Water and Flying type attacks, but somehow it knows Grass, Fire and Electric type attacks! That's not physically possible! Team Rocket decides that they must have this awesome Pokémon, so they, too, challenge Anthony. This time, however, Anthony panics and the truth comes out. Pelipper has been hiding Poké Balls inside its large beak. Rather than being disappointed, Team Rocket decides that this is an excellent opportunity. They blackmail Anthony and use his Pelipper for a new challenge. This time, trainers will lose their Pokémon if they lose to Pelipper. Team Rocket's latest hoax is very successful at first, and they con many trainers out of their Pokémon, but they soon get carried away. They fill Pelipper's beak up with so many PokéBalls that when Pelipper does a Water Gun attack, all of the PokéBalls spill out!
As our heroes travel on towards Rustboro City, they stumble into a forest filled with many different kinds of Pokémon. It turns out that the area is actually a Pokémon preserve, and it's looked after by a girl named Katrina. Katrina takes care of all of the Pokémon in the area and helps to nurse them back to health when they are sick. Max takes a particular liking to her Poochyena and he's determined to see it evolve before they leave the preserve. All of the Poochyena's companions who were born at the same time have already evolved, but this one Poochyena just doesn't seem ready. Max decides to coach the Pokémon and leads it out into the forest. Team Rocket has followed Max and they decide to play a trick on him to take the Poochyena. They claim to be researchers working on an evolution machine. Max is too smart to be fooled, but that doesn't stop Team Rocket from taking Poochyena. Luckily, Katrina and Ash show up just in time. This time Poochyena gets in on the action, too. That last battle turns out to be just what this little Poochyena needs – it evolves right before Max's eyes!
Ash, Pikachu, Brock, May and Max decide to cool off in a picturesque lake en route to Rustboro City. But they're not the only one's splashing around! The lake is actually home to a whole flock of Lotad. The Lotad seem to be having fun with their new friends, but a little girl named Natalie thinks that Ash and crew are out of line. She brings them back to the flower shop which her two older sisters run. There, Ash and the gang learn all about berries and the effects that different berries have on Pokémon. Brock promptly falls in love with the two older sisters, making little Natalie very jealous. In fact, Natalie isn't the only one smitten with Brock – a quirky little Lotad seems to have taken a liking to him as well. Natalie decides to win Brock's affection by finding a Sitrus Berry and she wanders off into the woods. She finds one, but a Beedrill wants it, too! Luckily, Brock arrives in time to save her from the Beedrill. Meanwhile, Team Rocket has decided to catch all the Lotad in the lake and it's up to Brock’s quirky Lotad friend and Pikachu to save the day.
Rustboro City is on the horizon, but they're not there yet. Ash, Brock, Max and May have just arrived at a Contest Hall. Janet and Chaz, two experienced Pokémon Coordinators, teach the gang all about Contests. Pokémon Contests are different from battles in that it's not the strength of the attack that matters, but the beauty of its execution. Winners get ribbons instead of badges. The gang decides that they want to try entering today's contest, but they're too late. All is not lost, however, because Chaz offers to teach Pikachu the Iron Tail attack. And Janet lets May assist her with during the contest. During the contest, Chaz and Janet both perform really well and make it to the final round. In the end, Janet's Beautifly steals the show! May is really impressed and she's determined to one day enter a contest herself.
As the gang continues to make their way towards Rustboro City, May spots a Wurmple that she's dying to catch – but she's not the only one with her eye on the cute little bug Pokémon. Jessie wants it, too. May ventures off on her own to catch her Wurmple, but Team Rocket follows and gives her trouble. Luckily, she gets some help from a trainer named Franklin. Meanwhile, Ash and Pikachu are practicing Pikachu's Iron Tail attack. A trainer named Franklin sees them practicing and challenges them to a battle. Franklin teaches Ash about double battles, which are common in the Hoenn region. With help from her new friend Franklin, May catches the Wurmple she wanted. When she and Franklin go to meet up with the gang, everyone is really surprised. The Franklins are actually identical twins – Forrest and Forrester Franklin! All is not lost for Team Rocket, however. Jessie manages to snag a Wurmple of her own after Team Rocket blasts off at the end of the episode.
Rustboro City at last! Now that Ash and friends have arrived in Rustboro City, they're taking a moment to sightsee. They bump into a schoolteacher, Roxanne, and her class on a class trip. The kids are about Max's age and one of them, Kenny, is afraid of Pokémon. Roxanne invites the gang back to see the Pokémon Trainer's School. Ash is anxious to get to his gym battle, but Roxanne persuades him to wait. As it turns out, Ash would have had to wait anyway. Roxanne is the Gym Leader, too! The Pokémon Trainer's School is pretty big and has all kinds of different classes. May is especially interested in a class on Pokémon Contests. Max decides to attend the beginners' class that Kenny is in. He's in the middle of battling the class show-off, Tommy, when the principal comes running in to tell them that the school's Poké Balls have all been stolen. Team Rocket strikes again! Kenny steps in and saves the day by telling Max which attacks will work best, and Tommy cooperates, too. When they work together, the kids are able to defeat Team Rocket and save the PokéBalls. Just to be safe, Roxanne's Geodude sends Team Rocket blasting off again. Now that Ash has seen Roxanne and her Geodude in action, he's really ready for his gym battle!
Pikachu is getting pretty good at its Iron Tail attack and that's a good thing. Ash is finally about to take on Roxanne, the leader of the Rustboro Gym. He's going to need all the help he can get to take down her Geodude. May, on the other hand, isn't really looking forward to the battle. In fact, she announces that she's not going to be a trainer anymore. She wants to become a Pokémon Coordinator and compete in contests instead. When the battle begins, it doesn't look like Ash has much of a chance. Roxanne's Geodude knocks out Treecko pretty quickly. It's all up to Pikachu. Electric attacks aren't going to help much against a strong Rock Type – but Ash is very clever and Pikachu not only brings down Geodude, but it wipes out Nosepass with its newly perfected Iron Tail Attack. Ash defeats Roxanne and receives his Stone Badge.
Max accidentally spills juice onto the Pokénav, causing it to spoil. He needs to find a place to have it quickly fixed while letting nobody know it's spoiled. He ends up meeting with the president of the Devon Corporation, makers of the Pokénav and everything else. The president gets interested in Max and offers his help to Max to repair the Pokenav. However, the tour into the corporate headquarters turns into a hunt for a spy who is after some of the company's research and they learn about two evil team members in the Hoenn region – Team Aqua and Team Magma.
Ash enjoyed meeting the president of Devon Corp. and learning a little about Team Aqua, a dangerous group of evildoers, but now he really wants to get to Dewford Island. Unfortunately, May's map is about 10 years old and they end up in a deserted part of town that used to be the port. From there they can see the new port, but it looks very far away. May goes off to look for someone with a boat and runs into Briney, a retired sailor, and his Wingull, Peeko. Briney offers to take the gang over to Dewford Island, but when she returns with Ash and the gang, Briney seems very angry and says that he has no idea what she's talking about. It's like he doesn't even recognize her. Meanwhile, Officer Jenny swings by and she tells them that Team Aqua is planning to meet up somewhere in the area and to be careful. Brock and May realize quickly that Briney might actually be in trouble – and they're right.
As Mr. Briney takes the gang to the closest Island, they are attacked by a gang of Sharpedo and are forced to stay on a deserted island. They must convince the Sharpedo that they do not want to harm them and also protect those same Pokémon from Team Rocket.
Eager to win the Knuckle Badge, Ash goes straight to challenging Brawly, Gym Leader of Dewford Town. However, Ash loses patience when Brawly goes surfing instead of battling. Finally, he gets his match, where Brawly's Makuhita evolves into Hariyama.
After James tricked Ash and friends to fish in an area so that Team Rocket could commit their usual schemes, the two sides had a battle until May sent out her Wurmple. Jessie sent out her Wurmple to show that it's better and then they had a riduculous argument, which resulted in the battle starting again, in which Meowth bumped into the two Wurmples. May and Jessie both take one and soon after, Pikachu blasted them off again, but then May finds out that the Wurmple she took isn't her Wurmple!
Team Rocket digs another hole, this time in Granite Cave, to capture the "twerps" but it only succeeds in separating everyone (Including Team Rocket)!
Ash chases down a mysterious Pokémon that keeps assaulting people on Dewford's beach.
After Corphish is injured following a Team Rocket encounter, Ash must rush his newest Pokémon to the Dewford Center-which is surrounded by a school of hungry Carvanha.
While in training, Ash and the others stumble upon a lake full of Mudkip under the watchful eye of an old man who is the protector of the Mudkip in the lake. Brock also catches a Mudkip of his own.
While walking through Granite Cave, the gang stumble upon Loudred in the middle of a long sleep. When it is accidentally woken, the gang are forced to run and find themselves separated from Pikachu, Treecko, Torchic, Mudkip, Silcoon, Lotad and Corphish. While the worried trainers search, the Pokémon begin to fight among themselves until they find themselves attacked by a group of Nuzleaf.
Ash and his friends accidentally stumble upon another Pokémon Trainer's Secret Base. Meanwhile, Team Aqua and Team Magma both attempt to take over the Secret Base and wind up in battle with one another
May and Jessie both blissfully await the day when they shall receive a Beautifly. However, Jessie is unaware that she will never have one, because her Wurmple became a Cascoon instead of a Silcoon.
Corphish's bad attitude showing no signs of improving so Ash plans to humble it a bit by putting a good scare into it deep inside an abandoned mine. Little does he know, however, Jessie, James, and Meowth have already infiltrated the mine.
Ash and friends get caught in a hurricane and must take a treacherous mountain path to reach safety. Also, Ash meets up with an apprentice of Gym Leader Brawley, who is in preparation for the upcoming re-match.
Ash's long-awaited rematch with Brawly of the Dewford Gym finally arrives. For the location, Brawly selects a secret sparring area he has hidden on a nearby island. Above and beyond this Gym Leader's ability and powerful Pokémon, the battlefield itself presents many unique challenges, most notably a huge geyser that erupts into the air without warning.
Ash and friends foil a Team Rocket kidnapping scheme on the high seas, but are then left high and dry themselves when Team Rocket's boat breaks down. Drifting with the tide, they eventually come to rest against an abandoned ship. On board, they meet one of the ship's original passengers, who has returned to search for the Marshtomp he was separated from when the ship first ran aground.
As May prepares for the upcoming Pokémon Contest, a passing retired Coordinator compliments her on her battling skills. On hearing that she is preparing for her first Contest, he invites her and her friends to his house where he keeps some items that could prove helpful to May's performance.
Impressed at how well they had raised their own Pokémon, Nurse Joy enlists Ash and Max to babysit the Treecko, Mudkip, and Torchic awaiting a Pokémon trainer just about to begin her first journey. The Torchic proves to be the most rambunctious of the group, and when Ash sends several of his Pokémon to gently coax it into obedience, he inadvertently causes the troublesome chick to evolve into a Combusken.
May and the others arrive in Slateport City, where she can compete in her first contest. Also compeating is May's new rival, Drew and a young man named Robert who uses Milotic.
Having at long last completed her Pokémon Contest, May suggests a day of recreation in Slateport City before moving on. While she and Brock shop in the city's famous market district, Ash and Max check out a local oceanic museum. What should have been a day of leisure, however, turns into one battle after another as both Team Rocket and Team Magma storm the very same museum in search of a rare rock discovered on the ocean floor.
While cutting through a mountain pass, Ash and friends decide to stop into the local Pokémon Center for directions. Imagine their surprise when they discover it vacated, with no sign of Nurse Joy. The plot thickens when they take it upon themselves to investigate and discover security camera footage of a Shriftry immobilizing Joy with Sleeping Powder before carrying her off. Their only clue as to Joy's location is a mysterious entry on Shriftry in the Pokédex, indicating that these Pokémon inhabit only trees that are over 1000 years old.
When Ash and friends get lost in a dark and foggy mountain pass, the first people they meet are Jessie, James, and Meowth of Team Rocket, fresh from their latest heist. Ash and friends manage to recover the stone the trio had stolen from a nearby lighthouse, but only in time to be themselves mistaken for the thieves.
The gang finally reach Mauville City, however Ash's Gym battle is forced to wait as the gang see an advert for a Pokémon Trick House, offering anyone who makes it through with a one year supply of Pokéblocks. May is eager to win the prize, so the gang decide to enter, and meet up with a girl and her Whismur. But when Jigglypuff decides to perform her song, things may get complicated for the gang, and Team Rocket too
Ash's third Gym battle with the electric master Wattson is full of surprises when, after an encounter with a robotic Raikou, Pikachu wins the match alone with super-charged Thunderbolts. However Ash's joy at receiving the badge disappears when Pikachu turns ill, and a depressed Wattson leaves Mauville City convinced he is a weak Gym Leader.