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A Work in Progress (but feel free to contribute) covering the Pokemon Franchise.

Games

Timeline #1

Recent History
  • July 20th 1969: Neil Armstrong becomes the first human to walk on the Moon.
  • A war takes place. At the end of it, American Lt.Surge and his Pokémon settle in Vermilion City and start a Pokémon Gym.
  • Mr. Fuji went on a archeological dig for Mew. Mewtwo is cloned from Mew and Mew gives birth to Mewtwo. Mewtwo later broke out, went rogue and burnt the mansion in Cinnabar Island. Out of atonement for this Mr. Fuji moves to Lavender Town and takes care of abandoned and orphaned Pokémon.
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  • The film Stand by Me is produced.
  • The Super Nintendo Entertainment System is released and proves to be extremely popular in Kanto.

Starting point of the Timeline - Gen I Era

  • A two boys, canonically named Red and Blue leave Pallet Town and events of Red/Blue/Yellow occur. Eventually, Red defeats Blue to become Champion of Kanto.

Between Generations

  • A volcano erupts on Cinnabar Island, forcing its inhabitants to evacuate.
  • The Kanto region champion Red retreats to Mt Silver to train in solitude, leaving Lance to act as Champion in his place. Furthermore, Lorelei and Agatha leave at this time. Their vacancies are filled by Karen, Will, and Koga.

3 Years Later - Gen II Era

  • A boy (or possibly a girl in Crystal version) leaves New Bark Town in the Johto and Kanto Regions Gold/Silver/Crystal. He/She eventually encounters Red and battles him on Mt.Silver. Red then leaves for parts unknown.
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Timeline #2

Beginning of Time
  • Arceus hatches from an egg in a vortex of chaos, and created the Universe.
  • Mew came to be, and descended into all other Pokémon.
  • The regions formed.
  • The war between Kyogre and Groudon happens in Hoenn.
  • The Ultra Beasts, a group of extradimensional Pokémon, emerge from mysterious rifts in the sky and attack Alola; the native Island Guardians battle furiously to keep them at bay.

100 Million Years Ago

  • Many Fossil Pokemon were widespread during this era. Archen in particular is believed to have been the ancestor of latter bird Pokémon.

3000 before Starting Point

  • The war 3,000 years ago in Kalos (a divergent point of the universes).
  • The Abyssal Ruins of Unova were built during this era.

500 Years Ago

  • The Guardian Deities of Alola fought Solgaleo and Lunala.
  • The first Spiritomb was created using 108 spirits of wrongdoers.
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  • Magearna is created by a scientist as a gift for his king's daughter.

Recent History

  • PokéBall technology Created, starting with Apricots from Johto, which eventually refined with the help of the Devon Corporation in Hoenn, the PokéBall Factory in Kalos, Silph Co. in Kanto and others.
  • New Pokémon species such as Lunatone and Elgyem are first discovered.
  • Team Rocket is formed in Kanto
  • Mr. Fuji went on a archeological dig for Mew. Mewtwo is cloned from Mew and Mew gives birth to Mewtwo. Mewtwo later broke out, went rogue and burnt the mansion in Cinnabar Island. Out of atonement for this Mr. Fuji moves to Lavender Town and takes care of abandoned and orphaned Pokémon.

Starting point of the Timeline - Gen III Era

  • The events of Ruby/Sapphire/Emerald (In Universe A) and Omega Ruby/Alpha Sapphire (in Universe B)
    • Ruby/Sapphire Universe doesn't make mention of the War or Mega Evolution, but is referenced in later games. While, Omega Ruby/Alpha Sapphire, don't mention previous game events, but instead show evidence of going to happen in the future. Since you could send Pokemon from Hoenn to Hoenn of the same time period, without causing Paradoxes, and since the franchise is Soft-Sci-Fi, if Sci-Fi at all, an alternate universe makes the most sense.
  • The Events of FireRed/LeafGreen and Colosseum (at the same time as Above)
    • Team Rocket Disbanded, Giovanni disappears to parts unknown.

Between Generations

  • A volcano erupts on Cinnabar Island, forcing its inhabitants to evacuate.
  • Team Snagem terrorizes the Orre region before being defeated by an ex-member named Wes.
  • The Kanto region champion Red retreats to Mt Silver to train in solitude, leaving Lance to act as Champion in his place. Furthermore, Lorelei and Agatha leave at this time. Their vacancies are filled by Karen, Will, and Koga.
  • Anabel, a Frontier Brain from the Hoenn of Universe A, somehow passes through an Ultra Wormhole and ends up in the Alola of Universe B, with no recollection of her past life.

3 years from starting point - Gen IV Era

  • The events of Diamond/Pearl/Platinum and HeartGold/SoulSilver take place.
    • Team Rocket reappears, becoming involved in various criminal activities across Johto. They are, once again, defeated.
    • One of Team Rocket's acts is to use a radio signal at the Lake of Rage to evolve the Magikarp into Gyarados. One Magikarp evolves too early and stays red as a Gyarados. This Gyarados is the subject of a T.V newscast in Sinnoh, which prompted two children to go search of something similar at Lake Verity, kickstarting their careers as Pokémon Trainers. These trainers would eventually save Sinnoh from Team Galactic.
    • Cyrus, using Team Galactic, tries to recreate the universe, but without emotion or spirit. After he fails, he remains in the Distortion World, a dimension created by Giratina.

5 years from starting point - Gen III Era

  • The Events of XD happen. Team Cipher disbands permanently.

At least 6 years from starting point - Gen V Era

  • The events of Black and White happen.
    • N, the leader of Team Plasma, summons a Legendary Dragon and commands the people of the Unova region to release their Pokémon. Shortly afterwards, he defeats the Unova Elite Four and Champion, before being defeated by a hero chosen by the other Legendary Dragon of Unova. He then learns that the Sage Ghetsis was using N and Team Plasma as a way to accumulate power. With Ghetsis defeated, N disappears along with his Legendary Dragon.

More than 7 years from starting point - Gen VI Era

  • The events of X/Y and Black/White 2 occur.
    • The Pokémon World Tournament is held in Unova. Gym Leaders and Champions from Kanto, Johto, Hoenn, Sinnoh and Unova, including Red and Blue attend.
  • Gladion flees the Aether Foundation, stealing one of the three Type: Null they'd created. His goals were to prevent Ultra Beasts from harming the Alola region and develop a bond with his new partner.

More than 9 years from starting point - Gen VII Era

  • The events of Sun & Moon happen (around 2 years after Black 2 and White 2 (and by extension X and Y), as Grimsley's concept art says).
  • The events of Ultra Sun & Ultra Moon happen. In an alternate version of timeline #2, Necrozma comes to Alola but is driven back to Ultra Space rather then staying. The appearance of the Ultra Recon Squad alters Sun and Moon's story by quite a bit.
    • Team Rainbow Rocket, a version of Team Rocket comprising of versions of past evil team leaders from timelines where they won due to no player character interfering with their plans arrives in Alola and takes over Aether Paradise. They are defeated by the player character.
    • In both versions of this adventure, the player character encounters Red and Blue, now adults.

Timeline #3?

Starting Point of Timeline — Let's Go Pikachu and Let's Go Eevee

  • History is the same as Timeline #2, but starts to diverge a little before the beginning, where Red, Green/Blue and probably Blue/Green begin their Pokémon training careers and go on their journeys through Kanto without encountering Team Rocket. The starting point proper begins with the player character receiving a Pikachu or Eevee from Professor Oak and progresses through the game as normal, Team Rocket included.
    • During the events of Let's Go Pikachu/Eevee, the player character meets a younger version of Mina, a Pokémon Trainer from Alola. Meaning that the game takes place at most 3 or 4 years before Sun & Moon/Ultra Sun & Ultra Moon. Necessitating a possible new timeline.

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