A/N: This would make more sense if you've read the other stories in order. PC: Apparitions, Global Warning, Meeting, and Healing all lead up to this story. Though it can be enjoyed without knowing a lot of the backstory, it helps.
Rui held the Snag Machine tightly and stared up at the Indigo Stadium. It had only been a few seconds since she and her new friends, Red, Silver, May and Brendan were teleported out of the area and to a safe distance. High overhead, a storm of epic proportions was spinning in a fury, bearing down on the stadium and the plateau. Within the Indigo Stadium, the legendary Pokémon of the world were fighting to stop the storm, using all their might to push the cell into the atmosphere and dissipate the clouds. With them was the man she loved and the world's best hope at salvation; Seth Evice.
Known to the Pokémon as Raykyoudon, to Cipher before its fall as Project: WSLY, to his friends and loved ones as Seth, the rebel Snagger from Orre was making his stand against the storm of his creation. As the super-legendary Pokémon he was designed to be, Seth had unwittingly unleashed a hellish maelstrom that would destroy everything. Now he was about to repair the damage he had wrought.
By going back to the beginning.
It was Rui who had told him to do so, placing in him all her trust and love and friendship. And in telling him to go back, they both knew she was making a tremendous sacrifice. The battle against the storm would likely kill him.
"It's not rising any higher! There's not much time left before the legendaries konk out and we all die!" May cried, raising her hand to shield her eyes as she watched the storm rage.
"We've got to trust that he'll pull this off!" Silver exclaimed, "We don't have much of a choice!" They continued to watch the events unfold. Jupiter and Pluto, Seth's twin Eons, stepped forward and whimpered. The Espeon and Umbreon feared the worst when a brilliant burst of light filled the air.
"What is that?" Red murmured as the glow within Indigo Stadium increased in brilliancy. Rui gasped and blinked.
"That's got to be Seth!" she exclaimed and cried out when the glow died, only to find it replaced by a golden spiral that rose from within the arena to the heavens, carrying the brunt of the storm with it. The twister didn't seem very solid, she could just about make out spaces within it that hinted at the tornado being formed of small pieces. But pieces of what?
"That's gotta be Raykyoudon's power!" Brendan exclaimed, "The bastard did it! Yeaaaah, Seth!" Red and the others cheered, fists pumping into the air as they realized the tornado was Seth's handiwork. Jupiter and Pluto cried sorrowfully, instinct telling them that the spiralling energy was all that remained of their master and friend.
Celebi and the other legendaries appeared beside them as they rooted for the spiral that climbed ever higher, growing wider and more scattered as it took in the entirety of the storm clouds. The tiny Grass-Psychic wailed in sorrow, reaching for the twister and catching Rui's attention.
"Guys! This isn't good! Celebi is crying!" she declared, "What's going on?!"
"Seth! That's Seth's energy! He's tearing himself apart! If he keeps it up and rises completely to the atmosphere, he'll never return!" Celebi howled, clawing at the air, "He's going to die! He's going to die and it'll be my fault! There's no way he'll come back then!" Red translated her words and looked horrified.
"You promised you'd come back, Seth!" Rui screamed at the twister, "I said to go back, but this is too far!"
"He's got to come down! He has to come back to Earth!" May exclaimed.
"But if he slacks off on the storm, it will come down with him and destroy the world!" Silver protested. Red scanned the heavens for a sign of hope and shook his head regretfully.
"I don't think so. Enough of it has already been torn away that the worst we'll get is a hurricane, but even that is going to cause major damage to Kanto and Johto." he murmured, "He's not going to be able to make it back. It's too much, too late."
"Let the rain fall! Red! Translate the words and call them out!" Celebi suddenly blurted. Red looked at her in confusion, "No time to explain! Do it!" Within moments of his translation everyone was calling to the heavens. With no idea of whether they would be heard or heeded, Rui and her friends cried the words until their voices grew faint. Finally, they saw the spiral of energy drop apart, raining down with the last of the storm from the evil machine called the Earth Seal. Golden bits blinked out of existence as they fell, dying one by one and taking more of their friend's life with them.
In the end, only one bit remained. The tiny golden bead made its way to Celebi's hand and she turned with a happy smile to her kind. She spoke to them in a commanding tone filled with hope and love and the three legendaries responsible for Seth's former existence roared out. Energy flowed from all three, collecting with the golden piece and forging a body within a misty white veil that concealed it. Seth was returning.
"She says we have to go back to the beginning." Red went on translating as the cloud suddenly flashed brightly and disappeared. "That's where Seth is. Where it all began, that is the beginning. The reason why Seth existed as the darkness, as the enslaved Raykyoudon. That was the beginning then, and it is the beginning now." He looked at Rui, "He's alive and he's at the place where it all began." He watched with the others as she looked down at the machine in her arms, then slid it on. She looked up at them fiercely, the Eons standing beside her with determination on their faces to match her own.
"Orre. The Shadow Pokémon Lab." Rui told them, "That was where Seth was created. It must be the beginning."
"There could be other beginnings. You have to take Seth's entire history into account." Red pointed out.
"Will you help me then? Will you come with me to Orre and to the Beginning?" Rui asked them, "Help me to find Seth, please!"
And the adventure continued for Rui and her friends...