The Scuffles of Legends (グラードンＶＳカイオーガ！（後編） Groudon VS Kyogre! (Part Two)) is the 6th episode of Pokémon: Advanced Battle.
Team Aqua has gained control over Kyogre and prepares to unleash its powers over the world's water levels. A Blue Orb possessed Pikachu releases Groudon from its entrapment and the two prepare to take on Kyogre in a battle to end all battles. Will Groudon and Kyogre destroy the world with their legendary battle or will Lance, Ash and his friends be able to stop the world's imminent destruction?
Shelly tells Archie that Kyogre has been released, though Archie planned that all along. He takes out the Red Orb goes up to the temple, though Maxie begs him not to do it. Team Aqua and Shelly send Walrein to protect Archie, using Water Gun to attack Team Magma. Tabitha and Team Magma send Mightyena to use Shadow Ball, countering the attacks. As Archie admires Kyogre, Team Aqua and Magma continue battling. Tabitha tells a recruit, who is Lance in disguise, to go with Maxie, who will have to stop Archie. Max, May and Brock hide and see the battle between these two forces. Team Rocket has blasted off to an edge of a cliff, wanting to be somewhere else. On a helicopter, Archie uses the Red Orb, commanding Kyogre to sink the land. As lightning cracks, Kyogre summons whirlpools. This terrifies everyone, including Team Rocket. Everyone tries to warn Archie that people are still on the island and the sea will flood it. Archie ignores them all, which crushes Team Aqua members.
Lance takes off his disguise, warning Archie will be controlled by the Red Orb. Archie ignores Lance and has Kyogre make tornadoes and thunderstorms. As both teams try to regroup, Lance warns the orbs were used by people to control the Legendary Pokémon's powers. The people grew more power hungry, and despite their wisdom, the power of the Legendary Pokémon was much more dangerous. Thus, the orbs were sealed to prevent their misuse. Maxie claims they analyzed the orbs and have deduced to control them to build a better world, though Lance denies those facts. Maxie, however, wants to know who Lance actually is. Ash watches over Pikachu, but an earthquake makes them fall to ground. Maxie also falls to the ground and Tabitha rushes to him. Pikachu wakes up, and being possessed by the orb, he emits electricity, then goes away.
As Brock, May and Max go to find Ash, they encounter Lance. Brock and Lance recognize each other, while May and Max are honored to meet him. Ash appears behind the hole of the plane, telling them that Pikachu ran off. Soon, they hear Shelly telling the troops to go to the temple, as a giant wave is approaching. Lance sends Dragonite to free Ash, using Dragon Claw to open the hole. Meanwhile, Team Rocket is astonished, as Team Aqua's submarine has washed up on the coast. Lance decides to go after Archie and asks the heroes to find Pikachu. Per Maxie's orders, Tabitha goes after the heroes. Shelly tells her fellow members to stay put until she gets Archie. Lance demands the Orb, but Archie continues to refuse. Archie uses the Red Orb, ordering Kyogre to attack Lance. Dragonite evades Hydro Pump attack and Lance's Gyarados uses Hyper Beam, but Kyogre uses Hyper Beam as well, negating both attacks.
Archie claims no force can stop him, and will soon control the world. The Orb is being absorbed into Archie and takes control of him, as he has blue marks. James wants to go away, but Jessie reminds Meowth and James they can still capture Groudon. They go to the place where Groudon is, but locked. Meowth thinks that if they were to anger Kyogre, it would attack them by summoning a wave. Next, the wave would push Team Rocket on the submarine with Groudon inside and everyone would be happy. James thinks it is possible, while Jessie compliments Meowth's plan. However, they are struck by Pikachu's electricity, as Pikachu is still possessed by the Blue Orb. The heroes goes after him, but Pikachu jumps to the submarine, where Groudon is. Team Rocket attempts to capture Pikachu, but are being blasted off by his attack. Lightning strikes, as the heroes, Maxie, Tabitha and Shelly watch Pikachu. Ash begs Pikachu to stop this madness. With Pikachu's power and the lightning it struck, Groudon feels the attack and awakens. The submarine explodes, which terrifies Ash what happened to Pikachu.
Everyone witnesses the eruption of a volcano. Groudon awakens, causing a beam of light to strike the clouds and stops the thunderstorm. Pikachu jumps onto Groudon's head, which relieves the heroes he is okay. Kyogre summons the waves to flood the island. May is terrified, seeing this is even a bigger wave than the last one. Max thinks they should go to higher level, but Brock thinks that the wave will flood the island and Groudon as well. Groudon attacks the waves with Solar Beam, stopping them. Maxie tells Tabitha they were fools to believe they could control as powerful as a Groudon. Shelly fears Kyogre is comes as powerful and worries about Archie. As Groudon walks with Pikachu into the sea, Lance goes to the heroes, realizing that Groudon wants to stop Kyogre. He states the orb absorbed into Pikachu was made to let Groudon ask Pikachu to help it fight Kyogre. Groudon waves its claw and launches a shock wave, which hits Kyogre. Lance tells the heroes to go away, but Ash tells he needs to stay behind to help Pikachu first, even if it means battling both Kyogre and Groudon.
Brock, Max and May decide to stay to help Ash, since they are a team. Kyogre attacks with Hydro Pump, but Pikachu stops it with Thunderbolt. Lance plans has Ash come with him on Dragonite, while the others go on his Gyarados. Lance plans for an opportunity to get Pikachu back, while Brock, Max and May have to distract Kyogre and Archie. Ash thanks them and promises to May he won't do anything crazy. Groudon uses Solar Beam against Kyogre, harming it. Kyogre pulls Groudon to the water, worrying Ash about Pikachu. However, Groudon comes back, retaliating with Mud Shot against Kyogre's Hyper Beam. May sends Beautifly and Brock his Mudkip. Mudkip uses Water Gun and Beautifly Silver Wind, attacking Archie's helicopter. Kyogre, per Archie's order, goes after them, so Gyarados, with Brock, May and Max on it, goes away. Groudon uses Solar Beam, hurting Kyogre and stopping the waves Kyogre tried to summon. With Kyogre severely wounded, the Red Orb leaves Archie's body. Archie falls, but Dragonite captures him in time. Groudon roars and the Blue Orb leaves Pikachu's body as well. y Pikachu unconsciously falls down into the ocean, so Ash dives after him. May, Max and Brock are shocked and try to get Gyarados to find them. However, Kyogre goes after Pikachu and Ash. Shelly tends to Archie, who gains consciousness back. Archie does not recall a thing, but Shelly promises everything is back in order. Ash appears on Kyogre, who did not attack him and faces Groudon. May, Max and Brock are happy Ash is fine, and Pikachu regains consciousness as well. Ash hugs Pikachu, while Brock sees Groudon battled against Kyogre, whose rage has vanished. Suddenly, the two Orbs go up in the air, merging and vanishing into dust. Maxie, Tabitha, Shelly and Archie watch as Groudon goes to the volcano and Kyogre dives to the depths of the sea. During the sunset, Max sees the lava from the volcano cooled off and created more land. Lance tells them that the legend repeated, as Kyogre and Groudon created the world again, by taking control of the land and sea. Lance notes the Orbs were vanished, marking that humans cannot control nature, especially not for selfish desires. This makes Ash wonder if he'll see Groudon and Kyogre once more.
- Featured Pokémon: Totodile, Feraligatr, Gyarados, Scyther
- Background music from Mewtwo Strikes Back, Power of the One and Spell of the Union is used.