More focused storyline. Ash & Leaf travel through Mt. Silver to get to Johto, with Ash finally getting Charizard's approval through their journies in the mountain. Upon arriving in Johto, Ash and Leaf start forming a new team in preparation for the Johto League and challenging badges, meeting a new friend named Ethan along the way who has dreams of being a Pokeathlete. Meanwhile, Jessie, James & Meowth prepare for the resurrection of Team Rocket. A mysterious boy named Silver becomes Ash's major new rival, and by the end of the series, with Jessie, James & Meowth having brought back Team Rocket, it is discovered that Silver is Giovanni's son. Giovanni, JJ&M are arrested by season's end. The League acts as the series's bookend once again.
His main rotation team:
In the PC, brought back occasionally:
Ash brings Pikachu, Charizard & Togepi with him through his journey through Mt. Silver. He roams through there until he can get Charizard to listen to him, going through many frustrating trials. Upon finally getting Charizard's approval (now he just greets Ash with a jubilant Flamethrower to the face), Ash decides to leave Mt. Silver and head to New Bark Town. His team is much different - he receives a Totodile for his hard work training Charizard from Professor Elm, who saw his performance in the league and is proud of his growth with Charizard. Soon after, he catches a Sentret which evolves into a speedy Furret. Heracross is caught much like in the Johto series, while he catches the over-happy (Exploding constantly) Pineco which Brock had in the series. His Togepi evolves into Togetic and is Noctowl's replacement, finally showing some strength in battle. Phanpy is received as an egg much earlier on and evolves into Donphan shortly before the League, while his bond with a lost Larvitar allows him to grow it to its evolved form. His Totodile evolves all the way throughout the series, forming a rivalry with Charizard, which causes tension between Ash & the fiery lizard again. By the League, Charizard and Feraligatr get over their rivalry and help Ash get a lot of wins. Ash gets to the Top 32 in the Johto League, faring worse than he did in the previous league, making himself feel down and blaming it on overconfidence as his Pokemon did a good job but he was too arrogant and clouded with his previous League's success to really focus and be aware of each team member's strengths.
Her main rotation team:
In PC, brought back occasionally:
Leaf only brings her Jigglypuff with her to Johto. This season explores her feelings a bit more for Ash, and her doubts as a Pokemon trainer. Upon arriving in New Bark Town, Ash's efforts in the League are rewarded by Professor Elm, who gives him a Totodile. Not recognizing Leaf at all from the League, she doesn't get a starter from him and is irritated because of it. She ends up catching a Chikorita, the Johto starter she wanted, all on her own, separating from Ash to get it herself. They reunite when she finally catches one, and she tells Ash that she's starting to feel like she shouldn't train anymore. While challenging gyms and catching new Pokemon and defeating Team Rocket throughout the series, we see Leaf looking into other options - perhaps acting as a lab assistant for Professor Oak, because she starts showing curiosity toward how Pokemon and evolution work. By the series' end, Leaf's League performance is much better than her last, and in a really tough battle, she actually defeats Ash. She makes it to the Top 8. Satisfied with her performance, but still not feeling complete with herself, Leaf decides to return to Kanto and take up that opportunity to be a lab assistant with Professor Oak. She thanks Ash for the opportunities they've had traveling together, and gives him a kiss, wishing him luck in the future.
A Pokeathlete from New Bark Town, who recognizes Ash & Leaf from their performance in the Indigo League. He gets his starter at the same time Ash receives Totodile from Professor Elm. Ethan starts off as an annoying fanboy who follows the pair around, until a battle between Ash & Ethan shows Ash is impressed with the boy's spirit. They later become friends at the Bug Catching Contest, where Ethan catches a Yanma, and the boy decides to travel with two of his idols. Ash often acts as a mentor to young Ethan, and Ethan takes part in a 'sidequest' of Pokeathlon competitions throughout the series, where Ash and Leaf cheer him on. Ethan's Shiny Politoed would be caught in an episode showcasing Shiny Pokemon, where Ash, Leaf & Ethan all compete to catch it, and in the end, young Ethan emerges victorious. At series' end, after helping Ash, Leaf and Silver defeat Team Rocket and watching Ash and Leaf's League performances, Ethan stays in Johto but promises to one day meet up with Ash and be stronger than before.
Silver is an ***, like his game counterpart. He is Ash's main Johto rival, seen as a crook and a thief and a sly devil overall. As the series goes on, we see his hatred for Team Rocket develop. By series' end, Giovanni makes his return and we learn that Silver is his son. Silver manages to defeat his father and is instrumental in his arrest. Silver makes it to the Pokemon League tournament and does some damage. After Leaf defeats Ash, he is the one to beat Leaf in the Top 8. He makes it to the Top 4.
Now leading the 'revolution' of Team Rocket in an attempt to bring Giovanni back, Jessie, James & Meowth are fully competent villains. They still have a silly streak, but are clear in their motives. They end up bringing Giovanni back by series' end, after many failed schemes to steal legendary Pokemon such as Ho-oh, Lugia, and the legendary dogs, but they are arrested alongside Giovanni.
A now much-matured Gary returns sporadically throughout the series, having now become the Gym Leader of Viridian City since Giovanni's disappearance. Due to his responsibilities as a gym leader, Gary doesn't challenge the Johto League, and instead returns throughout the series to offer Leaf the chance to become an assistant at his grandfather's lab like he is currently training to do. He manages to win her over after the League, and they return to Kanto together. Due to his maturity, Ash's comical fits whenever Gary does show up to offer Leaf a job at his grandfather's lab make Ash
look like the childish one in this series.
League conclusion: Ash makes it to the Top 32 but loses in his battle against Leaf. Leaf makes it to the Top 8 but loses to Silver. After her loss, Leaf is more satisfied with herself but still sees herself interested in Pokemon research. She decides to take up Gary's offer and return to Kanto, with a goodbye kiss and a wish of good luck to Ash. Ethan, meanwhile, decides to take up training in Johto but promises to meet with Ash once again and be much stronger when he does. Ash leaves Johto with just his Pikachu and heads off to Hoenn alone.