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The men carried Tobi far from the island, travelling in the shadows much like their former squad leader did in order to quickly jet the man back towards his home base in Northern Kanto. Tobi stopped the men with a raise of his hand as they were moving across a wide open plain in Hoenn. He used the small portion of strength he regained to pull two Pokeballs from his belt, releasing his greatest captures, Latios and Latias.
The two looked expectingly at Tobi as he took his time to gain his energy back to speak. He held the empty Pokeballs out to his men and they unceremoniously stomped them until they were nothing but broken messes. Tobi addressed the duo one last time.
"It's better off that you two roam free now, I don't have the power to protect you if the terrorists survive and come looking, or anyone for that matter. Go off somewhere that no one can find you, hide away or take a form that no one will suspect you in."
The Latios and Latias both gave a farewell as they agreed with Tobi's last command to them. They darted off high into the sky and did a loop for show before disappearing from view.