Ash and Harrison are left with only one Pokémon each. Both Charizard and Blaziken start off with powerful Flamethrower attacks, which collide to form a giant cloud of smoke. Ash then commands Charizard to use Flamethrower again, which Blaziken easily dodges by jumping high into the air. Taking advantage of Blaziken's inability to move freely in the air, Charizard tries a Dragon Rage attack, but Blaziken dodges, then counters using Quick Attack. Charizard flies upwards, though Blaziken still manages to hit him with Flamethrower. Blaziken follows up with another Quick Attack and Charizard is hit by a Fire Punch, but, unfazed, counters with Flamethrower, which lands a direct hit on the Blaze Pokémon.
Blaziken is ordered once again to use Quick Attack. As Charizard and Blaziken brawl it out, Ash commands Charizard to use Seismic Toss. Brock and Misty cheer as Charizard circles around in the air. As the smoke clears, Blaziken appears to be down. The referee prepares to call the match, however, Blaziken gets up. With both Pokémon tired out, Blaziken uses one more Quick Attack, which Charizard counters with Flamethrower. Charizard attacks again with Seismic Toss, but Blaziken dodges and smashes Charizard with a Blaze Kick, a move that Ash has never heard of before, dealing severe damage to Charizard. Charizard, sustaining the damage, unleashes a full-power Dragon Rage attack to meet Blaziken's Flamethrower attack. As the smoke clears, both Pokémon struggle to their feet. Harrison and Ash plead for their Pokemon to get up, and with encouragement, both of them do. Ash orders another Flamethrower attack, but Charizard proves to be too exhausted and collapses. Charizard attempts to get back up again, but this time, he is unable to do so, having been completely rendered unable to battle. With Charizard's defeat, Harrison has won the match and Ash is therefore eliminated from the tournament. Ash is left distraught from the loss, with all of his supporters being equally disappointed. Delia is particularly sad for her son, given all of his preparation, though Professor Oak reminds her that it was a fine battle.
Later, Ash and the others say goodbye to Squirtle, as it prepares to rejoin the Squirtle Squad with Officer Jenny. Professor Oak and Delia also head back to Pallet Town, and Charizard after a night's rest in the Pokémon Center to recover will be returning to Charicific Valley the following day. Meanwhile, Team Rocket seeks shelter inside their stall as a crowd of angry customers surrounds them and demands more Badges. Jessie and her teammates sit glumly inside as they wait for more supplies to arrive to meet the increasing demand.
In the next match, Harrison faces Jon Dickson from Sento Cherry Town. His last remaining Pokémon, Houndoom, is soon taken out by Jon's Rhyhorn. The referee declares Houndoom unable to battle and awards the match to Jon, ending Harrison's Silver Conference campaign. Ash and the others are shocked to see Harrison now lose. Brock figures that Blaziken was too injured from fighting Charizard yesterday, so Harrison did not want to risk its health any further, causing Ash to blame himself for Harrison's loss. That night, Harrison is sitting alone by the river, but Ash and his friends join him. Ash asks him about Blaziken, and Harrison reveals that Blaziken is going to be fine. Harrison turns his attention to Ash’s connection to the famous Professor Oak. Harrison explains that he has heard a lot about Oak from his mentor and friend, Professor Birch. He declares that Professor Birch motivated him to travel to the Johto region to experience new Pokémon and meet new people. Harrison recommends that Ash should visit the Hoenn region, and the sound of meeting new Pokémon instantly piques Ash's interest.
A sudden scream breaks the moment, so Harrison and the others rush over. They come across two girls who declare that some ghosts are troubling them. Misty and Ash are quick to realize that they aren’t ghosts. Brock reassures the girls and orders Ash to use his Noctowl, which he does. Noctowl uses Foresight and the ghosts are revealed to be a trio of Misdreavus. Suddenly, Gary comes in and explains that the Misdreavus appear to be looking for something. Misdreavus goes off somewhere, and the gang follows. They soon find another Misdreavus, who is stuck under a tree. With everyone's combined efforts, they lift the tree to free the trapped Misdreavus. Gary runs over and inspects the Misdreavus. Thankfully, it isn’t injured, and all of the Misdreavus happily depart. Gary explains that the Misdreavus actually live higher up on Mt. Silver, but must have been disturbed by the Silver Conference. Ash is pleasantly surprised by Gary's expertise. Gary reveals that he wants to be a Pokémon Researcher to uncover the mysteries of Pokémon evolution. He declares that the Silver Conference will be his last battle competition before wishing Ash all the best with his own battling pursuits. Gary gives Ash a wave goodbye before walking off into the distance. Brock and the others are happy for Gary, though the sudden change in direction leaves Ash speechless.
The next morning, the Silver Conference comes to an end with Jon Dickson becoming the winner of the Johto League Silver Conference. Mr. Goodshow presents Jon with the coveted trophy as the crowd cheers on. On the other side, Team Rocket are still waiting for the customers, but because the Silver Conference has come to a close, no customers can be seen. Suddenly, a huge group of people heads straight towards the building. But they weren't customers; they were none other than their old customers, who have now caught on to the scam. Team Rocket rushes inside the building and Jessie orders "Operation Rollout" to go ahead. Their stall building suddenly transforms into a robot, frightening the disgruntled customers away. Jessie declares the additional mecha features she added a success, and both James and Meowth agree.
Meanwhile, Gary decides to travel through Mt. Silver before heading back to Pallet Town. Harrison plans to continue on with his journey by traveling to the Indigo Plateau in Kanto. Ash declares that he and his friends will be making a stopover at Viridian City before returning to Pallet Town. As the different parties prepare to go their separate ways, Team Rocket rolls in with the mecha. The Rocket trio is thrilled to see the twerps and launch into their motto. James fires a coin missile that hits everyone but sends Ash and Pikachu flying. As Team Rocket raises an electric-proof net to capture Pikachu, Gary calls out his Blastoise and orders Hydro Pump, which cuts the net in half. Harrison calls on his Blaziken's assistance, and it uses Flamethrower, setting the robot building on fire. Pikachu delivers a Thunderbolt and Team Rocket, together with the robot building, is sent blasting off. Afterward, Harrison, Gary, and Ash's group part ways.