Mr. Stone/Manga/PA/History/ORAS

Mr. Stone and Steven lead an operation to prevent an incoming meteoroid from crashing into the Hoenn region. To assist him in this mission, Mr. Stone enlists the help of his old friends, Mr. Briney and Drake, as well as the aid of Ultima of Two Island, who is tasked with teaching the Hoenn Pokédex holders,, Sapphire, and , the ultimate moves. The three Pokédex holders are also given a Mega Bracelet, which they can use to activate Mega Evolution.

Once Sapphire and Emerald finished their training, Mr. Stone has Mr. Briney take everyone to the Sea Mauville, where a machine known as the Absorber is located. The next day, Mr. Stone and Steven use the Absorber on Sapphire's Chic and Emerald's in their Mega-Evolved states. The process drains the life energy of the two Pokémon and transfers it into a machine capable of transporting the meteoroid away known as the dimensional shifter, but also causes intense pain to Chic and Sceptile. Despite the scene horrifying everyone else, Mr. Stone and Steven continue with the process. After the dimensional shifter is filled with enough energy, the area is attacked by Zinnia and her small army of Team Aqua and Magma Grunts in order to destroy the shifter. Everyone fights off Zinnia and her allies, but a wild appears and uses its ring to warp Sapphire and the shifter to another location. After Ruby arrives to help, he manages to get Zinnia to leave by offering up his and Emerald's Mega Bracelets.

Afterwards, Mr. Stone and Steven are left behind on the Sea Mauville while everyone else goes off to find another way to stop the meteoroid. Dejected that his plans failed and friends abandoned him, Mr. Stone nearly gives up until Steven cheers him up by pointing out that Sapphire and the shifter have merely been transported somewhere else. They quickly receive a call from Professor Cozmo, who informs the two that Sapphire and the shifter safely arrived at Mossdeep City, but the Space Center is being swarmed by press members that were informed about the disaster that will strike Hoenn. Mr. Stone and Steven immediately head off to Mossdeep City to help with the press.

Upon arriving, Mr. Stone helps Professor Cozmo with the rocket that the dimensional shifter was attached to. Sapphire tells Steven that she senses Zinnia's presence and goes off to stop her from interfering with the rocket's launch. Sapphire and Zinnia's clash leads the two into battling on top of the rocket while it flies through the air. Eventually Sapphire is defeated, allowing Zinnia to destroy the shifter and knock the rocket into the ocean.

Later, Mr. Stone and Steven travel to Sootopolis City, where Zinnia was taken to after her attempts to get Rayquaza to join her ended in defeat. Mr. Stone attempts to apologize to Zinnia for the trouble he caused in attempting to control Rayquaza. Zinnia rejects this apology and claims that Mr. Stone is only trying to save face for his failures.