Disclaimer: I don't own Pokémon or Naruto. All I own is this idea.
This story will have some elements from Naruto.
Prologue
Among the mountains of Unova, a lone figure could be seen trudging in the deep snow. The figure is wearing a dark cloak that has two purposes: to provide warmth in the cold weather and to hide the person's identity. Floating near the figure is a shadow-like figure with cloud-like mist as it's hair. Near them is a cave opening where light can be seen flickering, inside. The pair continues to walk towards the cave when a sharp ringing came from inside the figure's cloak. The pair stopped walking, startled with the sudden sound. The figure reached inside his cloak and brought his XTranceiver to his ear.
"Hello?" The figure talked in a baritone voice.
"We.. We need your help now." A weak voice answered. The figure was startled, not recognizing the voice. "Who is this?" A sigh could be heard from the other line.
"It's me, Looker, of Interpol." Now the figure was intrigued. Why was one of the top agents of the International Police need his help? Surely an agent like Looker won't need help from him.
"Why? Why do you need my help? You know my specialty doesn't lie with police work." The figure answered. The shadow next to him perked when he heard police work.
Looker growled from the other line. "It's because of those Galactic Pests! My plan backfired on me, they have succeeded in creating a chain from the powers of Mesprit, Uxie and Azelf. They have also stolen both Adamant and Lustrous Orb! Please! We need your help. SHE needs your help!"
The figure was shocked about the news. Team Galactic? The group that had weird bowl-cut hair? They were actually successful in their endeavors? "What do you need me to do Looker? As I've said, I don't do police work." After a moment, he added, "How is she, and how is she dealing with the problem?"
"I have no more time! The Champion has already confronted Team Galactic at Spear Pillar! She's battling her way up as we speak! And I fear that besides all her might, the deities of Space and Time might be too much for her." Looker answered. "We need your help to defeat those two! Only you have the power!" And with that the line went dead.
The figure was frozen in his place. Cynthia? Alone against the whole Team Galactic? That might not be too much for her, just a random stroll in the park. But against Dialga and Palkia at the same time? Her chances to win are slim. With those thoughts in his head, the figure made up his mind. He faced the shadow, who was patiently waiting for the figure's order.
"Darkrai, we need to head towards Spear Pillar quickly. Use Kamui."
The shadow's eye flashed red, and a vortex swallowed the two.
A girl, around 17 years of age, wearing an all black attire, can be seen sprinting towards the top of Mt. Coronet, where the Spear Pillar is located. With her is a shark-like creature with fins in both it's arms and it's back. This was Garchomp, The girl's companion since she was seven years old. The shark was decimating Team Galactic Grunts's Pokémon left and right. Most of the grunts ran away from the mere sight of the Sinnoh Champion.
"It's her!"
"Why is she here?!"
"Is that even a Garchomp?!"
"Cynthia!"
Cynthia smiled to herself. It wasn't common for people to run away in terror from her. In fact, this would be the first time. She sprinted towards the summit of Mt. Coronet, with her Garchomp right beside her, when she saw about 30 grunts blocking her way. The grunts felt that power comes with numbers so they brought out all the Pokémons in their possession. Around 120 Pokémons, most of which are big fat purple cats and four-winged bats, were facing Cynthia and Garchomp. She got two Pokéballs from her belt, and released the Pokémons from inside. Two flashes of light were seen by the grunts, which turned into a Jackal-like creature with a spike on it's chest and a humanoid green creature with bouquets as hands.
"Lucario, Roserade, I'll leave this battle to you!" Cynthia shouted while she was grabbed by Garchomp, who dashed past the grunts.
At the Spear Pillar, Cyrus and his Commanders were setting up the equipment they needed to bring out the power of the Red Chain when a Pokémon landed in front of them.
"You are too late, Cynthia. With the power of the Red chain we crafted from Uxie, Mesprit and Azelf, Dialga and Palkia will be finally be free from the constraints of their own dimensions!" Cyrus shouted. "Mars, Jupiter, Saturn, stall the Champion." With that statement, he turned around and left.
Cynthia stared at the three Commanders, and sighed. Mars seeing this, saw red and brought out her most trusted Pokémon. "Trample that bitch Purugly!" And in a flash of light a tubby purple-almost black-cat appeared. Saturn and Jupiter both sighed at the redhead's temper, and brought out their respective partners. "Go, Toxicroak/Drapion!" A bipedal load and a behemoth of a scorpion appeared and roared.
Cynthia, not being bothered in the slightest, ordered, "Garchomp, front and center!" Garchomp immediately went in front of her trainer, shielding her from harm. Mars, seeing this shouted, "Purugly, use Ice beam to freeze that dragon!" Following her example, Saturn ordered, "Toxicroak, get in close and use Close Combat!" Jupiter said, "Drapion, charge a Hyper Beam, and fire when I tell you." The scorpion nodded and began charging a yellow ball of energy.
Cynthia seeing the beam of blue light quickly ordered Garchomp to use flamethrower to cancel the attack and said, "Garchomp, attack Toxicroak with Dragon Rush!" Blue flames quickly licked the dragon's body then without warning, Garchomp sped forward, intending to clash with toad. Saturn, seeing the rapidly approaching dragon, shouted, "Toxicroak, use Close Combat when Garchomp is within your reach!" Toxicroak stopped in his tracks and waited for his chance. Half a second later, the toad felt an intense amount of pain all over his body and blacked out. Jupiter, seizing the moment, ordered, "Fire at her Drapion!" Mars, following Jupiter's example ordered a quick Ice beam.
Cynthia seeing the powerful attacks nearing her partner, quickly ordered Garchomp to use Draco Meteor. Garchomp launches a large flaming meteor towards the yellow and blue beams of light. The meteor was stopped for a moment, but it pushed the attacks away, and it shattered, pelting the cat and scorpion with flaming debris, leaving them unconscious.
The whole mountain shook, and the three Commanders smirked. "Your time is up, Champion! Boss has already finished his preparations! The Deities, have arrived!" Mars shouted. She took out three Pokéballs from her belt and threw them to the air. The two other commaders, brought out three Pokéballs as well. Cynthia frowned and took out her three remaining Pokéballs, and threw them to the air.
"Go! Crobat! Gyarados and Sneasel!" The three commanders shouted simultaneously.
"Milotic, Spiritomb and Togekiss! Take care of this three. Me and Garchomp will go and face Cyrus!" Cynthia shouted. Milotic, the leader of the three trilled in her soft melodious voice, "Miiiiiii!" As if saying her agreement. Hearing her response, Cynthia sprinted towards the summit.
During her climb up the stairs, she was met with many tremors. As she approached the summit, she felt two intimidating presences waiting for her.
She was met with an insane laugh at the summit. Cyrus was standing before the two Deities of Time and Space. Dialga and Palkia.
"You were too late Cynthia! With the power of the two legendary dragons, this world will be reborn in my own design!" Cynthia was trembling at the feeling of the two deities before her. Dialga, the Dragon of Time, and Palkia, Dragon of Space. Two Pokémons that she thought was pure myth. She gave Cyrus a dark look. "What have you done Cyrus?! You have disrupted the balance of the worlds!" Cyrus stared back at her.
"Do I care?"
Those three words ticked her off. At that moment, all she thought that this man.. No. This monster has to be stopped at all costs. "Garchomp! Attack Cyrus! Extremespeed with Dragon Rush!" Garchomp seemingly appeared near Cyrus, covered with blue flames when Dialga and Palkia's eyes opened, and saw a creature near them. Seeing Garchomp as a threat, they attacked.
"Diiiiaaaaaaaa!"
"Paaaaaaaaaal!"
Garchomp was blown back with an invisible force and was knocked out. Cynthia was aghast. Her stongest Pokémon, was knocked out, just like that? Is this the power of a legendary?
Cyrus was laughing. "See that Champion?! Even your mightiest will fall!"
Dialga and Palkia suddenly felt the presence of each other, and suddenly started fighting. Dialga's diamond was glowing, powering up it's signature move, while Palkia's gems in it's shoulders shoulders were also glowing. Dialga released a beam of light from it's mouth while Palkia slashed the air facing Dialga while releasing a pink wave of energy. Their attacks met and they fought for dominance.
Dialga, sensed another presence near it, and saw Cyrus. Seeing him as a threat, Dialga fired a concentrated beam of light towards him. Cyrus was too stunned to move and was obliterated.
Palkia saw Cynthia kneeling down next to her fallen Pokémon, and it fired a yellow beam of energy at them. Cynthia was glued in her position, and suddenly, her past memories came flooding back to her. Scenes of training her Pokémon, her Gabite evolving, getting a Pokémon egg from her grandmother and a guy waving back at her walking towards the sunset. She was jarred out from her thoughts when she heard a familiar voice.
"Darkrai, Kamui!"