Fluttershy walks forward and attempts to enter the cave. She is stopped by Red slowly standing up and approaching her.
"Thank you for freeing me from Mewtwo's control." Red says as he reaches into his backpack. "Before you fight Mewtwo, I'd like to help prepare you're team." Red pulls out a yellow orb and some Potions and Revives. "If you'll let your Pokemon out, I'll heal them for you."
Fluttershy reaches into her backpack and pulls out her Pokeballs, letting her Pokemon out. Red gets to work reviving her fainted Pokemon as Fluttershy looks at the orb. Red finishes with Empoleon and Jigglypuff before turning to work on Pikachu, grabbing the orb in the process. "This orb is a Light Ball. It's a special item that only works on Pikachu." He says as he gives the orb to Pikachu to hold. "It increases a Pikachu's Attack and Special Attack." He says as he uses a Hyper Potion on Pikachu, instantly making it perk up. After finishing with Pikachu, Red moves onto Charizard and quickly sprays a Max Potion over it, fully healing the Pokemon.
"There. Now you should be good to go." Red says as he places the used items in a special pocket of his bag and stands up. Fluttershy returns her Pokemon and enters the cave with Red and Rainbow to find Mewtwo standing in front of the panel where Gloriosa had found the magical geodes. Mewtwo turns around and looks at Fluttershy with contempt in its eyes.
"Hmm. You are stronger than I expected." Fluttershy and the others hear as Mewtwo speaks to their minds. "I will allow you to battle me. Prepare to lose!"
Fluttershy takes off her backpack and opens it to reach for one of the Legendary Birds when the three Ultra Balls suddenly float out on there own as Mewtwo's voice reaches Fluttershy's mind again.
"I can't let you use those beings!" The voice says fearfully as the balls start to shake before unleashing their contents. The three birds flock together above the center of the arena as the ground starts to shake. Suddenly, a ring appears before Fluttershy and a white and blue bird Pokemon emerges from the ring.
"LUGIA!" The bird screeches as it looks up at the trio it reigns over, who nod at Fluttershy. Luiga looks back at her before it launches an Aeroblast at Mewtwo, causing a vortex of air to hit Mewtwo as Mewtwo looks on in fear for a moment before attacking with Psystrike, unleashing a severe jolt of telekinetic energy upon Lugia as Lugia suddenly causes time to temporarily stand still. After time starts back up, Mewtwo attacks by building up an orb of blue energy before it throws an Aura Sphere at Lugia. Luigi returns suit by engulfing itself in a bright light while Mewtwo attacks by launching a ball of pure shadow at Lugia. This knocks Lugia back as it unleashes the light in the form of Sky Attack, causes wings of light to collide with Mewtwo as Lugia collapses from the Shadow Ball.
"You can do it, Charizard!" Fluttershy yells as she throws out a Pokeball and the fire-flying lizard appears on the battlefield. Charizard looks back as Fluttershy touches the stone in her bracelet, which causes Charizard to Mega Evolve. As a bright sunshine appears in the cave, Charizard attacks with Inferno. This caused massive flames to erupt from Charizard's mouth and engulf Mewtwo, burning it. Mewtwo then suddenly stops in time as it receives a sudden psychokinetic jolt from Lugia's Future Sight. Mewtwo drops to one knee as Charizard uses Heat Wave to defeat Mewtwo.
"We-we did it!" Fluttershy says as she rushes forward and embraces Charizard before she walks back over to her backpack and pulls out an Pokeball and lobs it at Mewtwo, who enters the ball. A star emerges from the ball as soon as it hits the ground. As Fluttershy moves to puts the Pokeball into her backpack, she notices that the Legendary Birds are surrounding her. The birds start to speak to her.
"Zapdos!" ("We knew what Mewtwo had been up to.")
"Moltres!" ("And we knew that it would take a fellow Legend's help to beat him.")
"Articuno!" ("So when Mewtwo tried to remove us, we knew we had to bring master Lugia to help you.")
"Zap!" (Use a Pokeball and capture our leader. It will allow Lugia to survive this ordeal.")
The three birds let out a final screech that Fluttershy understood to mean "Please save our master." She reahes into her bag, pulls out a Pokeball and throws it at Lugia. As soon as the ball hits Lugia, it opens, drawing in the white bird before it closes and shakes in the air. The ball hits the ground and emits a star as Fluttershy walks over to it. She picks it up and puts it into her bag as the Legendary Birds land by her side, each one of them holding their respective Ultra Ball in their talons. They each drop their ball their owners feet and Fluttershy returns them before walking out of the cave with Rainbow and Red. Rainbow starts to walk with Red towards the campgrounds before she notices that Fluttershy is standing at the entrance to the cave with Charizard at her side.
"Fluttershy? You coming?" Rainbow asks Fluttershy as she sees Fluttershy climb onto Charizard's back.
"You go on ahead, Rainbow. I think I'll fly back." Fluttrshy says as Charizard starts to fly towards Fluttershy's house.