In the beginning, there was an endless void of chaos. But from that chaos emerged an egg, which gave rise to Arceus, the Original One.

Arceus then created Dialga, Palkia, and Giratina to control time, space, and antimatter respectively.

However, Giratina was banished to the Distortion World for its violence. After that, Arceus set out with Dialga and Palkia to create the universe. Dialga and Palkia retreated to their respective dimensions, while Arceus continued to build the world.

Next was the creation of the Lake Guardians, Uxie, Mesprit, and Azelf to control knowledge, emotion, and willpower.

Groudon was formed from deep within the earth while Kyogre rose from the pressure of the deep sea. Rayquaza was formed from the particles within the ozone layer. Groudon expanded the land while Kyogre rose the sea level. The two would become archenemies, and only Rayquaza could stop their battle.

The only other Pokemon from this time were Mew, who would evolve into all other non-legendary Pokemon, and Regigigas, who shaped the regions by moving the landmasses created by Groudon. Regigigas created Regirock, Regice, and Registeel from clay, ice, and magma respectively.

After creating the Adamant, Lustrous, and Griseous Orbs, Arceus fell into a deep slumber at the Hall of Origin in Sinnoh.

Years passed, and the Mews began to adapt to various environments, evolving into several different prehistoric Pokemon. Some went extinct following a meteor impact. The Pokemon population continued to diversify, but they were not alone. The first humans appeared and worshipped several legendary Pokemon, such as Regigigas. However, they feared his power and sealed him, along with his creations, away.

A few thousand years later, a war broke out in what would become the Kalos region. However, people used Pokemon to fight for them, leading to the deaths of many.

Among the fallen happened to be King AZ's Floette. Using the power of the legendary Xerneas, he revived his Pokemon, but granted both of them immortality. In the process of reviving his friend, AZ had to use Yveltal to take the lives of many Pokemon. However, even after Floette's revival, AZ was full of resentment. He transformed the machine into the ultimate weapon, and with Yveltal's power, ended the war. The damage caused was so destructive that it caused two major events: Giratina was free to travel to and from the Distortion World, and the Pokemon universe split into two separate timelines. In one (Universe A), the war never happened, but in the other (Universe B), the weapon caused meteorites to become Mega Stones.

In Universe B, meteor showers in the Hoenn region rained down upon the home of the Draconid tribe, creating Meteor Falls. They were overflowing with primal energy, which awakened Groudon and Kyogre. The two fought bitterly for the energy source, and there battle was stopped only when Rayquaza descended to stop them, and the two returned to their slumbers.

Time passed, and another meteor struck Hoenn, creating what would become the city of Sootopolis. Again, Groudon and Kyogre awoke, absorbing the energy released by the impact. They reverted to their Primal forms, and fought for twenty days and twenty nights.

The people prayed to Rayquaza for help, and once again, he faced his two subordinates. The spiritual energy from these prayers allowed Rayquaza to perform the world's first Mega Evolution.

With its newfound power, Rayquaza overwhelmed the two Primal Pokemon. Again, peace was restored, and a shrine was built to honour the saviour of Hoenn. The Draconids created the Sky Pillar, which depicted the events that had transpired and acted as a summoning point in case Rayquaza was needed.

Around this time, in the Unova region, two brothers ruled with a mysterious dragon. They debated what should define their kingdom: truths or ideals. They couldn't come to an agreement, and the dragon split into Reshiram and Zekrom to serve each of the brothers, while Kyurem was left as the empty husk of the original dragon. The two dragons fought, neither able to conquer the other.

Finally, the brothers set aside their differences and sealed the dragons away as the Light and Dark Stones in the Dragon Spiral Tower.

Many years passed, and Pokeballs were created. At last, people were able to catch and train Pokemon. Regional Pokemon Leagues and Gyms were set up. Several criminal organizations rose, including Team Rocket. Scientists of Rocket found the legendary Mew, managing to acquire and replicate a strand of its DNA. With this, they created Mewtwo for the sole purpose of battling. Upon discovering this, Mewtwo turned against its creators and went into hiding in Cerulean Cave.

In the Kanto region, two trainers set out on a journey to create the Pokedex. Red and Blue received their starter Pokemon, Charmander and Squirtle respectively, and their Pokedexes from Professor Oak. Red conquered the Kanto gyms while fighting Team Rocket. His team grew, and he faced the Team Rocket leader Giovanni at the Viridian City gym. He defeated him, and Giovanni disbanded his organization. Red then traveled to the Indigo Plateau, where he conquered the Elite Four at the Pokemon League. His rival, Blue, was the champion, and the two fought long and hard. Finally, Red's Charizard beat Blue's Blastoise, and Red was crowned as the new champion. He continued to fill his Pokedex, catching Articuno, Zapdos, and Moltres. Red then traveled to Cerulean Cave to catch Mewtwo. It was unlike any battle he had fought, with Mewtwo decimating his team. His last hope was his Charizard. In Universe A, they fought long and hard, and Red threw his Master Ball. In Universe B, the bond between the two, along with Red's Key Stone and Charizard's Charizardite X, allowed Charizard to Mega Evolve and overwhelm the legendary Pokemon.

Upon catching Mewtwo, Red departed for Mt. Silver for intense training.

In the Hoenn region, two trainers set off on their journeys. Brendan and May received their starters from Professor Birch, and set out to conquer the gyms of Hoenn. Along the way, they fought the organizations Team Magma and Team Aqua, who tried to expand the land and seas respectively. They awakened Groudon and Kyogre, who fought in Sootopolis. Brendan had to awaken Rayquaza to calm the two and restore peace. He then fought his way through the Elite Four and defeated the champion, Wallace.

In Universe B, only one of the two Primal Pokemon was awakened, and Brendan was forced to corner and catch Groudon/Kyogre in the Cave of Origin while it was in its Primal form. He caught the legendary Golems and set out for the Pokemon League. The Hoenn champion in this universe was Steven Stone, who was beaten. But his journey was not over yet, as a meteor was approaching.

When May's and Wally's Key Stones were stolen by Zinnia, Brendan chased after her to find her true intentions. She was attempting to summon Rayquaza to stop a meteor that threatened to destroy Hoenn. The two went to the Sky Pillar, where Zinnia explained the lore of Rayquaza, Kyogre, and Groudon. The next day, she proceeded to summon Rayquaza, but he was unable to Mega Evolve. Rayquaza then ate a meteorite that Brendan was carrying, and reclaimed the power it needed to Mega Evolve. Brendan battled and caught Rayquaza, who was taught Dragon Ascent soon after.

Brendan then fought Zinnia's legion of Dragon types. It was then that he unleashed the true power of Mega Rayquaza against Zinnia's Mega Salamence.

Brendan prevailed and rode Rayquaza into space. Rayquaza used Dragon Ascent to destroy the meteor, from which Deoxys appeared. Mega Rayquaza battled the alien Pokemon, which was soon caught by Brendan.

By the time he returned, however, Zinnia had left.

In Johto three years later, Ethan got his starter Pokemon, while Giovanni's son Silver stole one. Ethan conquered the gyms of Johto while defeating the re-banded Team Rocket once and for all, while also catching Ho-Oh/Lugia.

He conquered the Pokemon League and then defeated the eight gyms of Kanto. Professor Oak deemed him ready to face Red atop Mt. Silver. They battled ferociously, but in the end, Ethan won. Red left to explore the other regions.

In Sinnoh, Lucas and Barry set out on their journeys while also fighting Team Galactic, who aimed to recreate the entire Pokemon universe. Team Galactic created a Red Chain from the Lake Guardians, which would allow them to control Dialga and Palkia. After summoning the time and space Pokemon at the Spear Pillar, their success was inevitable. But the banished Giratina appeared and freed the two.

Giratina took the team's leader, Cyrus, to the Distortion World with Lucas and the Sinnoh champion Cynthia chasing after. He beat Cyrus one last time, then faced Giratina. The Renegade Pokemon was a difficult foe, but eventually was caught by the young trainer. Lucas beat Sinnoh's Elite Four and faced his toughest opponent, Cynthia. The battle was long and hard, but Lucas came out on top.

A few years later, Hilbert left on his journey with his starter Pokemon in Unova. Along the way he fought Team Plasma, headed by the mysterious N. N had befriended Reshiram while Hilbert obtained the Dark Stone. After conquering the gyms and Elite Four, he faced N. It was here that Zekrom awakened from the Dark Stone. Hilbert caught the legendary dragon and fought N's Reshiram with his Zekrom.

N had a change of heart and left with Reshiram upon his defeat, and Team Plasma was disbanded. Hilbert took on Alder and became the new champion. Similar to Red, Hilbert left soon after.

However, Team Plasma returned two years later. A new trainer, Nate, rose to stop them while conquering the gyms of a revamped Unova. This time, Plasma, headed by Ghetsis, planned to use Kyurem to conquer the region.

Ghetsis attempted to use Kyurem to freeze Nate, but N and Reshiram saved him just in time. Ghetsis used the DNA Splicers to fuse them, creating White Kyurem.

Nate battled and defeated the dragon, separating Kyurem and Reshiram. He then faced and beat Ghetsis, who gave up one final time. Nate made his way through Victory Road and the Elite Four, defeating the new champion, Iris. He then entered N's castle and received Reshiram as a gift. Nate then battled and caught Kyurem, obtaining the DNA Splicers. He could now create White Kyurem if he wished. He then entered the Pokemon World Tournament, where he fought Red from Kanto.

In the Kalos region, Calem and Serena set out to beat the Pokemon League. Along the way, they fought Team Flare, who planned to use the power of Yveltal to destroy the world. With the power of Mega Evolution, they fought the organization and arrived at their base. They found the ultimate weapon, powered by Yveltal's cocoon. Yveltal awoke and fought Calem, who caught the Destruction Pokemon. He then fought Flare's leader, Lysandre, and beat him for the last time. Calem then beat the Elite Four and champion Diantha after fighting Serena.

In the Alola region, Sun set off with his Greninja on his Island Challenge. He received a starter from Professor Kukui and fought Team Skull and the Aether Foundation on his journey while also traveling with Lillie, who carried a Cosmog with her. He also fought the mysterious Gladion, who was Lillie's brother. Aether's leader Lusamine planned to use Cosmog to open up an Ultra Wormhole to another dimension. She succeeded and proceeded to do so after Cosmog evolved into Cosmoem. This released several Ultra Beasts into Alola, who were held off by the Island Guardians. At the Altar of the Sunne/Moone, Cosmoem evolved into the legendary Solgaleo/Lunala, who helped Sun and Lillie travel to Ultra Space. There, Lusamine awaited them and was beaten by Sun. Lusamine was knocked unconscious, and Guzma took her to a hospital. Sun, Lillie, and Solgaleo/Lunala returned to Alola, where Sun fought and caught the legendary.

After fighting Gladion one last time, Sun took on the Elite Four and became Alola's first champion. However, he was challenged by Kukui and won. Lillie left for Kanto to start on a journey of her own while Sun caught the Island Guardians, assembled Zygarde-Complete, and helped Looker and Anabel from Hoenn in Universe A, who was teleported to Universe B by an Ultra Wormhole, find the Ultra Beasts. After, Sun caught Necrozma. He then went to the Battle Tree, fighting the Trial Captains, Wally, Cynthia, and even Red and Blue.