The building begins to collapse on the swimmer and the blind boy, prompting a timely rescue from Phoebe as she arrives. She puts the blind boy on the phone with Steven, and Steven gives the Champion's cloak to Wallace, accepting the call. The boy reads part of a braille slab Steven entrusted to him, but there is a break in the slab and he cannot read the rest of it. Steven is internally horrified, wondering if they are doomed.
Meanwhile, Winona and Flannery find Professor Starstone tied up in the abanded Team Aqua Hideout. They bring him onto the Pokémon Association Airship HQ ("Bachoon") and Winona instructs the injured Flannery and Wattson to remain there while she travels to Sootopolis. Wallace, in his aircar, is doing the same.
Ruby and Sapphire arrive in Sootopolis, and Maxie and Archie float up to Groudon and Kyogre respectively. Ruby and Sapphire send out their starters, attacking Maxie and Archie, but their attacks are easily repulsed.
Maryann and Tyler arrive on Absol in time to see Kyogre and Groudon attacking each other. Seeing Ruby and Sapphire, lying vulnerable nearby, Maryann begs Absol to do something, and Absol acquiesces, using Magic Coat to protect them from danger. However, Absol refuses to do more, making Maryann realize that Absol is an embodiment of nature and will not interfere in human disputes—as this battle is the fault of humans.
Wallace and Winona, just arriving, agree with Maryann's conclusion. The two gym leaders fly down to retrieve their students, who are far apart from each other, and both of whom have lost hope. Ruby and Sapphire beg their teachers to leave while they can, causing Wallace and Winona to snap at them, telling them that they are carrying the future on their shoulders and asking if they can bear to lose their loved ones.This prompts separate confessions from Ruby and Sapphire. They admit to having met someone in their pasts—Ruby is unaware that the girl he met was Sapphire, and Sapphire is unaware that the boy she met was Ruby—whom they wronged deeply. Norman was about to take his gym leader test and Professor Birch had come to Johto with Sapphire to offer his support. Ruby and Sapphire had only known each other for a few days, but were already best friends. One day, they were out playing and were attacked by a Salamence. Desperate to protect Sapphire, Ruby attacked the Salamence ruthlessly, driving it off, but in the process sustained a bloody wound and terrified Sapphire with his aggression.
Both express regret over the event: Ruby for scaring and tainting her, and Sapphire for being a burden and reacting like that. After that, both of their fathers become distant, Norman off training after failing his gym leader test and Birch engrossed in research, leaving their children feeling abandoned. Ruby and Sapphire resolved to change themselves—Ruby becoming dedicated to beauty, and Sapphire to strength—so that they could someday meet again and show how they have changed.
In the present, Ruby and Sapphire decide to keep fighting.
Winona, noticing that Sapphire's fragment of Meteorite has been growing hotter, mentions it. Wallace realizes that the Meteorite must have the power to negate the power of nature—considering that it stopped Mt. Chimney —and they set up a way using reflection to direct the radiation from the Meteorite to hit Archie and Maxie in the foreheads, where the Jewels are. They succeed, and cause an enormous explosion that engulfs all of Sootopolis.