Timeline

Prehistory
This information is based primarily on the study of fossils and other archaeological remains. Some of this information is also based on scientific research.
 * Millions of years before Generation I:
 * Earliest known prehistoric Pokémon exist. It is possible that the Mew population may have decreased at this stage, as they slowly gave way to other Pokémon species.
 * First humans appear in the Pokémon world.
 * At some point after the Iron Age, Regigigas is sealed away in Snowpoint Temple, and Regirock, Regice and Registeel are sealed away at various points across the Hoenn region.
 * At some point 300 million years ago, an ancient version of Genesect was born. Team Plasma later used its DNA to create an infinitely stronger version ofGenesect with cybernetic technology.
 * At some point 10,000 years ago during the last Ice Age, the Mamoswine population flourished, then decreased when the Ice Age ended.
 * 3000 years before Generation V:
 * The Relic items are created.
 * 2500 years before Generation V:
 * The Relic Castle is built.
 * 1500 years before Generation I:
 * The earliest known system for writing is developed and used at the Ruins of Alph, Tanoby Ruins, and Solaceon Ruins. Archaeologists are currently unsure whether the nearly identical Unown preceded or succeeded the writing system, but it is assumed they share some sort of connection.
 * The Farfetch'd population decreases due to overhunting.
 * Magikarp population mutates and becomes weaker.

Shadow Era

 * Shadow Arceus takes over the world and makes a Shadow army and enslaves the Human race
 * Arceus chooses a Hero with a high amount of Aura to defeat Shadow Arceus
 * Omega takes on Arceus' training to defeat Shadow Arceus
 * The Light Alliance is formed and goes to war with the Shadow Legion
 * Shadow Arceus takes his highest ranking General (Zeta) and gives him the ability to use the Shadow Powers at a supernatural rate
 * Omega makes a sword with his Aura to destroy Zeta
 * Omega Destroys Zeta and defeats Shadow Arceus

New Era

 * After Shadow Arceus' defeat they started a New Era to show a New step for man and pokemon
 * Not much else is known about this Era

Recent history
This information is based on historic records. Ecruteak City*Hundreds of years before Generation I:
 * The legends of Pokémon Ranger: Guardian Signs's past.
 * c. 700 years before Generation I:
 * Bell Tower and Brass Tower are constructed in Ecruteak City, and Lugia and Ho-Oh perch at their tops.
 * c. 500 years before Generation I:
 * The first Spiritomb is sealed in the Hallowed Tower for its unforgivable misdeeds.
 * The Cianwood City Pharmacy is built.
 * c. 400 years before Generation I:
 * Azalea Town in Johto is struck by a long-term drought. After bringing the rain back once again by yawning,Slowpoke gains an honorable position in that town.
 * The Pokémon move Toxic is invented by a ninja.
 * c. 150 years before Generation I:
 * Brass Tower burns to the ground, killing three Pokémon inside. Lugia flees to the Whirl Islands, Ho-Oh resurrects the three as the legendary beasts and flies off in search of a pure-hearted Trainer.
 * The first Pokémon League competitions take place.
 * c. 200 years before Generation V:
 * Village Bridge is constructed after the river flooded the area.
 * c. 100 years before Generation V:
 * The warehouses of Nacrene City are constructed.
 * Klink begin to appear in Chargestone Cave.
 * c. 50 years before Generation V:
 * Elgyem is seen for the first time when it appeared from far in the desert.
 * 1969:
 * First humans land on the Moon.
 * 11 years before Generation I:
 * Red is born.
 * Leaf is born.
 * Less than 10 years before Generation I:
 * The ferry S.S. Tidal is constructed.
 * The first Pokémon created by scientific engineering, Porygon, is created.
 * Rotom inhabits an abandoned mansion in Sinnoh.

Contemporary history
From the Pokémon games:
 * Some years prior to Generation I:
 * A team of scientists discover a new Pokémon (at the time) deep in a jungle in Guyana, South America on July 5. They name the Pokémon Mew on July 10. Mew gives birth, the only known case of a live Pokémon birth (possibly due to the scientists' genetic experimentation), and the scientists name the newborn Mewtwoon February 6. Mewtwo escapes from and destroys Cinnabar Island's Pokémon Mansion on September 1 and then goes to Cerulean Cave. At some point after Mewtwo's birth, Mew goes to Faraway Island.
 * Mr. Fuji, the writer of the Pokémon Mansion journals, goes to Faraway Island and leaves a message on the island's sign on the 6th of September, October, November, or December (depending on which of these months appear in the message) sometime after Mewtwo's escape.
 * After leaving his message in Faraway Island, Mr. Fuji goes to Lavender Town and has lived there ever since.
 * Sabrina's gym is declared the official gym of Saffron City after a Pokémon battle between Sabrina and the leader of the Fighting Dojo.
 * Giratina returns to the Pokémon world.
 * The Battle Frontier opens in Hoenn.
 * One year prior to Generation I:
 * Professor Rowan goes to Kanto to research the myths of the region.
 * Generation I/III:
 * The events of Red, Blue, Yellow, FireRed, LeafGreen, Ruby, Sapphire, and Emerald:
 * Red leaves Pallet Town on his Pokémon journey after their rival, Professor Oak's grandson, Blue. After getting the eight badges of Kanto, defeating Team Rocket along the way, he challenges Kanto's Elite Four, then its current Champion, none other than Blue himself. After defeating Blue, Red becomes theChampion, then ventures to the Sevii Islands to eradicate Team Rocket and help Celio to connect his Pokémon Net Center to the Hoenn region.
 * Brendan/May leaves Littleroot Town on a Pokémon journey shortly after moving to the Hoenn region from Johto by saving the local Pokémon Professor from an attacking wild Pokémon. At first, there is a deep-seated rivalry with Professor Birch's son/daughter, however, later on, the rivalry is with Wally instead. After defeating Hoenn's eight Gym Leaders and, with the help of Rayquaza, calming both Groudon and Kyogre, released from their banishment by Team Magmaand Team Aqua, respectively, he/she challenges and defeats Hoenn's Elite Four and current Champion, becoming the Champion him/herself, much to the astonishment of Birch's child.
 * Between Generation I/III and Generation II/IV:
 * The events of Pokémon Colosseum and Pokémon Ranger.
 * Eruption of the volcano on Cinnabar Island causes destruction of many areas on the island.
 * Blue takes the position of Gym Leader in the now empty Viridian Gym.
 * Red leaves to Mt. Silver, training day and night, leaving Lance to act as Champion, while Lorelei returns to her home in Four Island, and Agatha retires from her position as a member of the Kanto Elite Four. This leaves three vacancies on the roster for Elite Four.
 * Two of these vacancies are filled by Karen and Will. The other is filled by Koga, who abdicates his position as Gym Leader to his daughter, Janine.
 * Extensive research confirms the existence of Steel and Dark-types in the region of Kanto. (The events of FireRed and LeafGreen retcon this discovery and say that they had always been known as Generation III and I are considered to take place contemporaneously. This is backed up by HeartGold and SoulSilver, when Jasmine's pre-battle speech was changed from the subject that the Steel-type was recently discovered.)
 * Baoba leaves Kanto when its Safari Zone is closed and begins planning to open a new Safari Zone in Johto, as a replacement.
 * A Pal Park is opened in place of the Kanto Safari Zone.
 * Miracle Cycle moves from Cerulean City to Goldenrod City.
 * Groudon and Kyogre retreat to the region of Fiore to rest after their battle.
 * Giratina returns to the Distortion World.
 * A new Battle Frontier is built in Sinnoh and Johto.
 * Blaine relocates his gym to the Seafoam Islands due to his gym on Cinnabar Island being destroyed by a volcanic eruption.
 * After Generation I/III:
 * Humans abandon the PokéPark.
 * The Sky Prism breaks.
 * The events of PokéPark Wii: Pikachu's Adventure.
 * Three years after Generation I/Generation III (Generation II/Generation IV):
 * The events of Gold, Silver, Crystal, Diamond, Pearl, Platinum, HeartGold, SoulSilver, Pokémon Ranger: Shadows of Almia, and Pokémon Ranger: Guardian Signs.
 * Ethan/Kris/Lyra leaves New Bark Town on an errand for Professor Elm, bonding with his/her starter Pokémon on the way. A red-haired boy steals one of Elm's three Pokémon, and challenges him/her as Ethan/Kris/Lyra's journey across Johto continues. A revived Team Rocket, using plans formulated three years prior, enrages many Gyarados, including a red one, at the Lake of Rage as they proceed to take over the Goldenrod Radio Tower in a desperate attempt to contact Giovanni. As they are defeated, the leader vows to never again re-form Team Rocket, and Ethan/Kris/Lyra continues to gather Johto's badges, eventually gaining all eight and traveling to the Pokémon League at the Indigo Plateau in Kanto. After defeating the Elite Four and their Champion, Lance, Ethan/Kris/Lyra then heads to the Kanto region to challenge its eight gyms, which have changed from three years prior. After gaining all eight of their badges, for a total of sixteen, Professor Oak declares him/her ready to travel to Mt. Silver, where he/she meets and defeats Red.
 * Lucas/Dawn and Barry leave Twinleaf Town in an attempt to see a Pokémon like the recently reported red Gyarados in the nearest of Sinnoh's lakes, Lake Verity. After being attacked by a wild Starly at the lake, and using one of Professor Rowan's Pokémon to fend off the attacker, (apart from in Platinum canon, where they receive their starter Pokémon before actually reaching the lake) their journey begins in earnest, and both Lucas/Dawn and Barry challenge the Sinnoh region's eight gyms to gain the badges necessary to challenge the Pokémon League. Along the way, however, Lucas/Dawn is brought into many conflicts with Team Galactic, whose leader, Cyrus, wishes to remake the entire universe in his image with the powers of the legendary Pokémon Dialga andPalkia. Defeating the team and calming Dialga/Palkia/Giratina, Lucas/Dawn challenges Sinnoh's Elite Four and Champion, Cynthia, and becomes Champion him/herself.
 * Hayley, a friend of Bebe, opens up a Pokémon Ranch.
 * Approximately two years after Generation II/Generation IV:
 * Cipher and Team Snagem return in the Orre Region, and create XD001, a supposedly unpurifiable Shadow Pokémon, but their plans are thwarted by Michael. Meanwhile, Dr. Kaminko and Chobin invent Robo Groudon and Robo Kyogre, and Professor Krane invents the purification chamber, where Shadow Pokémon can be purified more easily.
 * Between Generation II/IV and Generation V:
 * The Team Rocket Grunt who stole the Machine Part returns to Unova intending to reform Team Rocket there as he previously stated. He later falls in love and has a son, moving to Icirrus City.
 * Caitlin leaves the Sinnoh Battle Frontier and returns to Unova, becoming an Elite Four member.
 * Team Plasma, under N, creates Genesect in an attempt to create the strongest Pokémon in existence by altering an ancient insect Pokémon with cybernetic upgrades.
 * A few years after Generation II/Generation IV (Generation V):
 * The events of Black and White.
 * Hilbert/Hilda along with their friends Cheren and Bianca receive their very first Pokémon in the bedroom of Hilbert/Hilda's house in Nuvema Town fromProfessor Juniper. The three decide to leave Nuvema Town and go on a journey across their region of Unova, with Cheren wanting to learn as much about every kind of Pokémon possible and Bianca going against the wishes of her dad. Upon arriving in Accumula Town they encounter the nefarious Team Plasmawho announce their plans for Pokémon liberation to seperate Pokémon from humans. Hilbert/Hilda then battle Team Plasma's leader, a mysterious man known only as N who claims Pokémon are his friends. Hilbert/Hilda make a journey across the land of Unova challenging all eight gyms and earning all eight badges. After earning the eighth badge, they travel to the Pokémon League where they defeat the Elite Four. Upon defeating the Elite Four, they discover that N has already defeated the champion Alder and promtply summons his castle, destroying the Pokémon Leauge Castle. Ghetsis, one of the members of theSeven Sages reveals that he had the plan to seperate people and Pokémon so that he could be the only person in the whole world with Pokémon. After defeating N and Ghetsis with Reshiram/Zekrom N becomes sorry for all his wrongdoing and releases his dragon of legend. Hilbert/Hilda, Cheren, and Bianca continue their journey in Unova and get recruited by an undercover officer codenamed Looker to discover and arrest the remaining six of the Seven Sages. After the arrest of all six, Hilbert/Hilda returns to the Pokémon League, re-defeats the Eilte Four, then challenges and defeats Alder, becoming champion of Unova.

Prophecy Era

 * Leaf and Red get married though as it turns out Leaf was a descendent of Zeta and Red was a descendent of Omega.Though Leaf does not revert when she learns of her History
 * Gray and Magma are Born
 * Shadow Pokemon start to wake up and the Shadow Legion almost completely wakes Shadow Arceus
 * Magma betrays Gray and joins the Shadow Legion
 * Gray becomes the leader of the Light Alliance and receives Omega's sword
 * Shadow Arceus fully awakens and War brakes out again