On the Team Rocket airship, Red and Green are shocked to hear Giovanni tell them that he wants to help save the planet from the meteor. Giovanni activates a projector, showing live footage of Kyogre, Groudon, and Rayquaza working together to destroy a falling meteorite. Blaise is shocked to see Maxie fighting alongside Archie, but Amber reminds him that Maxie cannot carry out his plans if the world is destroyed by a meteor. Giovanni reveals that he is fighting for the same reason—he will never be able to take over the world if there is no world to take over. Red is angered, unable to believe what Giovanni is saying, but Green advises him to focus on the meteor. They continue to watch the footage.
Holding onto Rayquaza with all of their might, Ruby and Sapphire try to break up the meteorite. Seeing everyone struggle against one meteorite, Maxie becomes concerned about what it will take to destroy the meteor itself. To make matters worse, parts of Archie and Maxie's bodies begin to disintegrate. They realize that their time is dwindling, but are still determined to do what it takes to destroy the meteorite the best they can.
The meteorite is broken up into small rocks that come hurtling back toward the ground. Kyogre and Groudon are battered with them, and are knocked unconscious. When Blaise and Amber see that Maxie and Archie are injured, they hurry out of the airship, flying down with the help of Blaise's Swellow. When they reach Maxie and Archie, they are horrified to see their bodies break apart. Amber asks what is happening to them, and the two begin to explain.
Four years ago, when Maxie and Archie absorbed the Red and Blue Orbs, their life forces depleted and they were no longer able to inhabit their bodies. Through a flashback, they explain that after losing their physical forms, they are given the suit of armor named Eternity, and the sword named Instant, two items that can prolong life. However, there is only one set, and the two are forced to fight each other for it. After losing, Maxie finds himself in a mysterious dimension, and is joined by Archie after he was defeated in the Battle Frontier. Both are without a physical form, and somehow merge into one. One day, an opening appears in the dimension, and a mysterious voice calls out to Maxie and Archie. After going through the opening, the two reawaken at the Ruins of Alph and are told to go to the Kanto region to learn about Mega Evolution, as well as acquire the Red and Blue Orbs to connect with Groudon and Kyogre. As Maxie and Archie wither away in the present, they agree to join forces in another time, and urge Blaise and Amber to protect the world.
Through the projection on the airship, Red, Green, and Giovanni watch as Blaise and Amber mourn their former bosses. Red notices that Kyogre and Groudon have turned back into their regular forms, and are no longer moving. Red yells for Giovanni to come up with a plan, unwilling to see the world come to an end.
As Ruby and Sapphire continue to ride on Rayquaza's back, Ruby notes that it is still restless, despite the fact that the meteorites have stopped falling. Sapphire takes the Green Orb from Ruby's hand and holds it to her heart. She appears to go into a trance, which only stops when Ruby calls her name. Sapphire grabs Ruby's arm and taps on his hand, communicating that Rayquaza is seeking more power. Ruby remembers the photo he took of the mural at Sky Pillar, and shows it to Sapphire. She pieces together that Rayquaza must want to Mega Evolve.
Suddenly, a figure swoops down just above Rayquaza, and Ruby and Sapphire barely have time to dodge. Looking up, they see Zinnia riding on her Salamence. Calling on the spirit of Lorekeeper Aster, Zinnia prepares to fight.
