Out on the stormy sea route 133, Gabby and Ty gasp in shock when they see the two giant energy spheres containing Ruby, Sapphire and the evil teams charge towards a north-eastern direction, which is apparently the same place where Absol is taking them. Ty manages to map out a route on his laptop, and after closely examining all the possible destinations that lie along it, realizes that they are heading for Sootopolis, the mysterious city sitting at the crater of a volcano where legends rest.

Ty explains to Gabby that Sootopolis is also the only city which intersects the borderline created between the opposing drought and heavy downpours affecting the two ends of Hoenn, and Gabby feels certain that it is where the two ancient titans will eventually clash. She remarks that Ruby and Sapphire are under extreme danger in that case, and decides to contact the Pokémon Association Chairman and Captain Stern immediately.

High up in the association's airship Ba.Goon, Captain Stern listens with horror as Gabby informs him about the imminent clash of Kyogre and Groudon. The Mt. Pyre old couple, who are also on the airship, overhear the conversation, and gasp that their greatest fear is coming to pass, that the slumbering ancient titans will finally awake.

The Chairman gets confused about the old couple's words as Groudon and Kyogre have long been awakened from the Seafloor Cavern, but the old woman explains that they are referring to the second awakening. It turns out that the titans' rise at the Seafloor Cavern was only limited to the physical plane, which was the first awakening, and the two have yet to awaken in the mental plane, which is the second awakening. In order to achieve this second awakening, the titans must head to Sootopolis where they will do so at the Cave of Origin.

The old man adds that Mt. Pyre and the Cave of Origin are deeply connected, in the sense that the two mystical jewels, the Red and Blue Orbs, will also be drawn to where the two titans are. If that happens, Groudon and Kyogre will fully awake in both physical and mental planes, and shall inevitably relive their prehistoric battle, the fight which will destroy and consume everything.

At Sootopolis, the whole city is caught up between the two extreme weather effects, with the southern part thundering with rain, and the northern half sizzling with heat. Within moments, Groudon breaks through the mountainous borders on the north, as Kyogre surfaces through the underwater opening from the south, finally coming face to face with each other in the central lake of the city. The two titans waste no time upon laying eyes on their rivals, and immediately engage in a fierce clash which throws the whole city into a turmoil.

Meanwhile, at Lilycove City, Brawly's Hariyama has blasted Hank and his two Slugmas out of the museum through a big hole on the wall. With its opponents weakened, Hariyama follows up with a knockoff to slam them against the street walls. Just then, the Slugmas drop two hair pins they have been holding, and Brawly recognizes them as Tate and Liza's. He realizes that they must have been defeated by Hank earlier, and demands to know what the man has done to them.

Panting against the wall, Hank grins that he taught them a lesson with his fire illusions while snatching the two orbs at Mt. Pyre, and Brawly presses him for their current location. But Hank weakly laughs that Brawly should care for himself first, and says following the mighty power he and Hariyama used to blast off Slugmas' fire attacks earlier, he wouldn't be able to stand much longer. Hank adds that sadly, he himself has no strength left to fight either, but he together with the two other FireHeads have already accomplished their goal in clearing a path for Groudon to mentally awake at Sootopolis's Cave of Origin, which the titan should have doen so by now.

The flames created by Hank's Slugmas gradually start to engulf him, and the man smirks that he should really compliment on Brawly's brutal force specialty, as no other strategies have managed to defeat his fire illusions before. Hank and his Pokémon then disappear with the flames, and Brawly tries to stop him, but quickly finds that he is indeed completely drained of all strength, and passes out on the ground.

Nearby, at the Cover Lily Motel, Courtney pops her bubblegum, and waves goodbye to Roxanne before disappearing in burst of flames. Roxanne cries over her fallen Nosepass, and remorses over the fact that they have failed to stop Groudon from advancing.

On the abandoned ship, Shelly's Ludicolo blasts Flannery's Vulpix with yet another naturepower, which manifested as a thick bundle of vines, and the six-tailed fox collapses to the ground unconsciously. Flannery rushes up to pick up her Pokémon, and Shelly grins that their battle is finally over. The Team Aqua subleader remarks that while their goal was simply to clear all obstacles to Kyogre's advance, which they have already succeeded, she finds it necessary to deliver one final fatal blow just to show off their power.

Up in the air, Winona sees that Flannery is in danger, and orders Altaria to use take down on Matts, knocking him and his Vibrava into the sea while she herself jumps down to shield the Lavaridge gymleader. Shelly smirks that it doesn't matter how many opponents she has as her attacks are able to cover every corner, and orders one final naturepower from Ludicolo. However, to her surprise, the kappa Pokémon fails to unleash the attack, and she demands to know what it is doing.

Flannery puts on a grin, and wonders if Shelly notices the growl Vulpix let out before the battle. She reveals that it was a grudge, and Shelly realizes that it is the skill which locks down the opponent's last attack which fainted it. Flannery hollers that Ludicolo will not be able to use naturepower anymore, and claims that her Vulpix has bet its own body to disable the attack. Feeling humiliated, Shelly yells that it doesn't make a difference to her as they have already won, and begins to take off on her Vibrava. Matts asks for help as he struggles with his fainted Vibrava in the stormy seas, but Shelly ignores it and tells him to take care of his own business.

Flannery attempts to give chase, but Winona stops her. The Fortree gymleader points out that they have not only failed to stop Kyogre's advance but have lost Wattson as well. She does not want to lose anyone else, and Flannery understands what she means. Flannery looks over to the spot where Wattson fell earlier, and a sense of sadness washes over her as she remembers the old man's humour.

Suddenly, a column of water blasts out from the sea into the sky, and Flannery and Winona gasp in astonishment when they see that Wattson and his Electrike have been propelled out of the waters. Flannery realizes that it is the attack waterspout, and a giant Wailord slowly surfaces, which Winona recognizes as Sapphire's Wailulu. Winona is surprised but thankful that it has followed her all the way from sea route 126 after Sapphire dove down to the Seafloor Cavern.

Flannery quick checks that Wattson is alright, and the old man is already starting to joke on how a waterspout managed to shoot him out. Winona wonders where the Team Aqua subleader who defeated Wattson went, and a cuboidal machine is without warning thrown onto the back of Wailulu. Winona picks it up to see that it is a navigation recorder of some sort, and reads its data to discover that it is actually from the Submarine Explorer 1, which began its journey at the open seas near Lilycove, went all the way down to the Seafloor Cavern and finally resurfaced on sea route 134.

Flannery thinks over the route of the vessel, and suddenly realizes that the open seas near Lilycove may actually be the headquarters of Team Aqua, where Prof. Cozmo is probably held captive at. Winona agrees to the possibility, and the three gymleaders begin to sail to Lilycove on Wailulu. Hiding himself behind a tree on the abandoned ship, Sean wonders if he did the right thing to hint them on Team Aqua's headquarters.

At the same time, Wallace is still fighting against Tabitha at the Lilycove Department Store. His Whiscash, Philippe, uses tickle to lower Torkoal's attack and defense, while his Luvdisc, Elizabeth, showers the place with a watersport to lessen the power of fire attacks. Wallace states that Tabitha will have no chance in winning and tells him to call it quits, but the big man is not ready to give up yet and thinks hard to come up with a plan.

Suddenly, a painful look appears on Tabitha's face, and all the muscles in his body begin to spasm. His eyes widen with a look of emptiness, and without warning, he throws himself against Wallace like a wild beast. The Sootopolis gymleader manages to dodge and wonders what has happened, but the big man continues to give chase, and Wallace hops up to the roof top of the department store. However, Tabitha swiftly follows, and grabs Wallace by the neck to hurl him against the vending machines for drinks.

Watching the beastly movements of the man, Wallace fails to figure out what is going on, and a voice suddenly comes on to say that it is the after effect of having come into contact with the orbs that control the titans. Wallace recognizes the voice and looks up, but then Tabitha starts to advance again and lashes out to grab him. A Metagross is quickly sent out to deliver a meteor mash onto the floor, and the attack throws Tabitha off his feet, knocking him out temporarily.

Even more certain after seeing the psychic steel Pokémon, Wallace tells his old friend that he has been waiting for a long time. Standing on his Metagross, Steven spreads his white cape and apologizes for arriving late for their pact...

Thanks To Coronis For Writing this for us