Hearing that the true culprits behind Hoenn's catastrophe are manipulating the destruction from the Seafloor Cavern, Sapphire grits her teeth in anger, and without warning, lifts off on Tororo. Surprised by the girl's sudden reaction, Winona quickly gives chase on Altaria, and demands to know where she is going. Sapphire hollers that she will not let anyone tamper with the peace of her homeland, and now that she knows where the liable ones are, there's nothing to stop her from hunting them down. She reaches for the pokeball of Wailulu, and sends the giant Wailord out onto the raging ocean. Together with the Mt. Pyre old couple, she dislodges from Tororo, and switches her mode of transport to surfing. Winona hops off Altaria to join them, and Sapphire hurriedly inquires about the location of the Seafloor Cavern. The Fortree gymleader remarks that the quickest way to go there will be to cut across sea route 126, and continue heading south in the direction of Sootopolis, but then she also reveals that the underwater cave lies at a depth which ordinary man power cannot reach, and Sapphire instantly feels a sense of defeat washing over her.

On the barren ground north of Fortree, Roxanne and Brawly are doing all they can to fight down Groudon's rampaging. Hoping to stump the land titan in its movements, Roxanne orders a rocktomb from her Graveller, but Groudon easily blocks it off, and hurls the giant boulders right back at them. Brawly grunts that they will need stronger attacks to hurt it, and has Machoke unleash a focus punch, but before the fighting pokemon could make contact, Groudon delivers a powerful swap and sends it crashing into the floor. Roxanne exclaims that their assaults didn't even manage to touch Groudon, and thinks hard to come up with another strategy. Meanwhile, the ancient pokemon lets out a growl into the sky, and further powers up the drought effect its ability conjures.

On the abandoned ship, Kyogre throws the sea into a turmoil, and causes Wattson and Flannery to flinch from the gigantic tidal waves. Wattson hollers that his expert type is supposed to have an advantage over Kyogre, and hurriedly orders Manectric to use charge and fill itself with the atmosphere's static electricity. The blue canine then fires off a mighty shock wave, and hits the sea titan square-faced. But before Flannery and Wattson could rejoice over their success, Kyogre shrugs off the attack, and gradually emanates a soft glow from its body. Flannery exclaims that it has raised its own special defence by calm mind, and is surprised that the rampaging creature has the intellect to safeguard its own weakness.

Back on the refuge liner in Slateport, Captain Stern, Gabby and Ty stand helplessly on the deck, and watch as the raging sea slowly eats up the whole city. Stern hears his name called, and looks up to see Wallace descending in his air-car. The two have a quick hand shake, and Stern thanks Wallace for helping them out in rescuing the citizens. He then inquires about Steven's current location, but the Sootopolis gymleader says he hasn't heard from him for quite a well. Surprised that Ruby isn't with Wallace, Gabby wonders where he is, and Wallace explains that the boy is at the emergency medical centre. He remarks that he is currently on his way to take the mother and child he saved earlier to the centre, and invites Stern, Gabby and Ty to come along, saying that he himself will need to contact the other gymleaders and learn about the latest happenings once he has access to a visual phone system.

At the city's emergency medical centre, Ruby slowly opens his eyes, and finds himself in bed. He looks around to see many other injured people in the room, and quickly remembers about losing consciousness after his failed attempt to call back Mimi. Struggling to climb onto his feet, he slowly walks around the place and spots the President of the Pokemon Fab Club alongside with the shipyard manager Dock. The two men appear to be suffering from a severe cough, and Ruby realizes they are inflicted with injuries beyond those from the flooding.

Just then, he hears Wallace's voice coming from the next room, and turns around to see four people coming towards his direction. He quickly dashes behind a wall to hide himself, and soon sees that accompanying his teacher are Captain Stern, Gabby and Ty. Overhearing their conversation and concerns over Hoenn's current status, it occurs to him that he is once again the only one who is shunning away from the situation. As always, he has opted to stay detached from the happenings before him, and shield his face from the spotlight while everyone else is giving all they can. The thought quickly puts a gloomy shade over his face, and he starts to wonder if he should have been less evasive afterall.

Accessing the visual phone system in the centre, Wallace hurriedly establishes connection with Winona, and is surprised to learn that the Fortree gymleader is currently on sea route 126 with Sapphire. Winona explains that the big catastrophe they feared has begun, and says the legendary ancient pokemons, Kyogre and Groudon, have both awakened, which stuns everyone who is listening. She adds that Roxanne and Brawly are holding down Groudon while Wattson and Flannery are battling Kyogre, and Wallace quickly offers to join either one of the combats.

Winona bitterly admits that the gymleaders' forces are in desperate need of complement, but their main concern actually lies elsewhere. Wallace wonders what she is talking about, and Winona explains that evil people are controlling the two ancient creatures from the Seafloor Cavern, and the only way to stop Hoenn's destruction is to head to the underwater cave and take down those culprits. Stern, Gabby and Ty exchange a horrified look as they realize the two evil teams have indeed aimed for trouble in reaching the Seafloor Cavern, and Stern hollers that with Submarine Explorer 1 and its special engine starter both stolen, there exists no other possible ways to reach that deepest region of Hoenn which is inaccessible by man power alone.

Behind the wall, Ruby listens intently, and suddenly gets the feeling that he has forgotten something important. He spots Sapphire on the phone system visual screen next to Winona, and sees the rock-like fish the girl is carrying. While his first impression is that he has never met the odd pokemon before, he gradually gets convinced that he has seen it somewhere once. As the words 'deepest region', 'impossible', 'inaccessible by man power' echo in his head alongside with the image of Sapphire's Relicanth, he suddenly recalls Mr. Briney's words and the old drawing he showed him on the boat. And then it becomes clear to him. The ancient deep sea pokemon that possesses the ability to reach a depth of the ocean that humans alone can't get to, the pokemon that Sapphire is holding in her arms…

Thanks To Coronis For Writing this for us