In the deepest seas of Hoenn, Ruby and Sapphire hold tight onto Relili the Relicanth as it takes them to the Seafloor Cavern with its dive ability. The two young trainers soon arrive at their destination, and throw themselves out of the water at the small lake located right at the entrance of the underwater cavern. Landing on safe ground, Ruby and Sapphire pant to catch their breath, and are relieved that they have finally made it.

As they recover from their long voyage, thoughts and concerns begin to flood their minds. Sapphire wonders to herself how long they have been diving, and gets the feeling that even though it seemed merely hours, they could well have taken days to reach where they are.

On the other hand, having spotted the collapsing Submarine Explorer 1 on their way down, Ruby has trouble figuring out why the vessel was damaged and ponders on the possibility that those who came down to the cavern are already returning above ground. Without saying anything, he worries that they have arrived too late, while Sapphire silently wonders what lies in the ominous caves ahead of them.

Suddenly, Sapphire realizes with a start that she is still holding Ruby’s hand, and frantically shakes herself lose. With her face turning a deep shade of red, she hollers that although she trusted Ruby about Relili’s powers, she still hasn’t forgotten what happened at Fortree, and says Ruby will be wrong in thinking that they would fight alongside each other. However, Ruby ignores what she says, and puts on his glasses while pointing towards the entrance of two tunnels in front of them. Sapphire quickly picks the left one and tells Ruby to take the right, but Nana without warning pops out from its Pokéball, and holds Sapphire back by pulling on her bagpack with its mouth.

Sapphire demands to know what it is doing, and Ruby barks that they are dealing with a situation way different from any previous ones, and that it is important for them to stick to each other. He says Nana must have sensed something, and is telling them not to enter the tunnels, but Sapphire protests and tries to wiggle free. Ruby remarks that Nana has an adamant nature, and tells Sapphire to give it a rest as the Mightyena will not easily change its mind.

Just then, Nana senses something getting close, and leaps in front of Ruby and Sapphire while glaring into the two tunnel openings. Ruby quickly orders it to identify the enemy with odor sleuth, and Team Magma members start charging out from the left cave with a Shuppet, Bagon and Numel, while Team Aqua members come out from the right one with a Duskull, Corphish and Lotad. Calling out their own Pokémon, Ruby and Sapphire get into a combative stance and prepare to fight.

Meanwhile, water continues to gush into the collapsed Submarine Explorer 1 as the vessel slowly rises towards the sea surface. Inside the flooded control room, Tabitha hollers that Sean needs to push harder on the metal door to prevent it from giving way, while he himself struggles to block the holes on the deformed wall. The big man commands Torkoal to speed up their ascend in pumping out its light density smoke, and says they should reach the surface very soon.

However, the submarine all of a sudden collapses completely under the powerful underwater currents, and sea water rushes in to sweep the two men off their feet. Taken by surprise, Sean struggles to breathe and quickly loses consciousness. Tabitha, on the other hand, manages to hold his breath, and pulls on Sean by the wrist while forcing his way up against the water resistance.

Above ground, Hank happens to be flying over the seas on his Swellow, and is shocked when he receives an emergent SOS signal from Tabitha on his Pokégear. Hurrying over to the source, he spots part of the collapsed Submarine Explorer 1 floating on the sea surface, and sends out his Armaldo to save his companion. The fossil Pokémon quickly dives into the storming seas to pick up the two men it spots, and brings them back onto the collapsed body of the submarine.

Hank then hops off Swellow and rushes over to tend to Tabitha, at the same time realizing that he has also saved one of the Team Aqua admins. With Tabitha still unconscious, Hank takes the man’s memory firelighter which stores everything he has seen, and learns of how Team Aqua snagged the Blue Orb from them, as well as the fact that Sean was betrayed by his own team leader. Hank thinks of how horrible it must be to be abandoned by his own team, and decides that he shall leave Sean alone and let him deal with his own business later on.

He then has Armaldo surf with Tabitha on its back while he himself embarks on Swellow again, and resumes heading to where he intended to before receiving the big man’s call for help. Tabitha soon regains consciousness, and wonders where they are going. Hank explains that their minions have reported to him about gymleaders thwarting Groudon’s activity on route 121, and they need to stop any interferers from meddling in Team Magma’s work.

At the Mossdeep Space Center, Courtney makes another bubble with her gum as she steps her foot on the injured bodies of the befallen scientists and researchers she knocked down earlier. Just then, her Pokégear beeps, and she answers to find Hank calling. She informs him that Groudon has indeed been slowed down in its rampaging, and Hank grunts that the gymleaders seem to be doing quite a good job. He remarks that he’s currently on his way to route 121 with Tabitha, and says it will be easier to handle things if they arrive as a team. Courtney says she’s just having some fun at the Mossdeep Space Center, and agrees to meet them later on sea route 124.

Back at the Seafloor Cavern, Chaka, Tororo, Ronono and Phadodo have knocked down all the Team Aqua members and their Pokémon, while Zuzu, Popo, Nana and Coco have taken care of the Team Magma ones. Suddenly, two voices come on to swear killing off all intruders that get in their way, and Ruby and Sapphire turn around to see Archie and Maxie with evil grins on their faces, each holding one of the mystic jewels in their hands...

Thanks To Coronis For Writing this for us