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Description
The Pokemon Timeline in The Crossover Game is divided into three universes. Although events in each universe take place simultaneously, the time placement in each universe is different, reflecting on the year that the first game of each rebooted Generation was released in Japan. (Generation I timeline begins in 1996, Generation III timeline begins in 2002, and Generation VI timeline begins in 2013).
You may curious as to the reasoning behind the different timeline placements. This is simply an in-game explanation for why some games, though they follow the same plot, seem to be more technologically advanced than their counterparts. (Such as Red/Blue having primitive PC storage boxes, FireRed/LeafGreen needing to link a supercomputer in order to trade with Hoenn games, and Omega Ruby/Alpha Sapphire supporting Wonder Trading and advanced PC storage boxes, among other tech).
Despite the different placements in time, each universe follows a simultaneous history, though there are key differences in each universe. The three universes are referred to as the "Classic Pokemon Universe" (or "CPU", also known as "Monochrome Universe"), the Pokemon Shared Universe (shortened to "PSU"), and the "Mega Stones Universe" (shortened to "MSU"). There is a fourth universe known as the Real World, which is based on the real world and as such, Pokemon is just a series of video games that began in 1996 and continues to the modern day.
Note: If a Pokemon game is missing from this list, such as Silver Version or Pokemon Pearl, it is because I don't own that game or have plans to buy it. The canon within The Crossover Game reflects on my video game collection and the games I plan to buy or have played before. Additionally, if some of the story elements I list don't match up with the actual games or if some games follow a different order than you'd expect them to, keep in mind that this is a fanfiction, and does not reflect entirely on the official Pokemon canon.

Classic Pokemon Universe (Monochrome):
This universe reflects on the Pokemon games released for the Game Boy, Game Boy Color, and Nintendo 64.
1996: The plots of Pokemon Red, Blue, and Yellow take place around the same time as Pokemon Stadium. The Mewtwo that appeared in Pokemon Stadium is the same Mewtwo that is later captured by Red. Unlike most alternate timelines, Red, Blue, and Yellow's storylines all follow virtually identical plots, with the only differences being Red's choice of Pokemon in his party, and Yellow's alternate storytelling (Pikachu starter, fighting Jesse and James, etc.)

1999: The plots of Pokemon Gold and Crystal take place at the same time as Pokemon Stadium 2. Here is where the timeline splits, even though both stories follow the same overall theme. In the Pokemon Gold timeline, Gold is the hero of the story, while the Pokemon Crystal timeline focuses on Kris becoming the heroine. Both stories end with a battle against Red on Mt. Silver. The events in Johto also lead to the discovery of Steel and Dark type Pokemon, and these Pokemon later migrate to Kanto.

Post-1999: Since no future Pokemon games are able to connect to Generations I and II (excluding Pokemon Bank with the 3DS versions of RBY), the story of this Pokemon world is cut short, and it is believed that the other regions and 500+ species of Pokemon simply don't exist in this universe. This reflects on Nintendo's original plans to end the Pokemon series after Gold and Silver.

Pokemon Shared Universe:
This universe reflects on the games released for the Game Boy Advance, GameCube, Nintendo DS, and Nintendo Wii.
2002: The events of Pokemon FireRed and LeafGreen take place, followed concurrently by the events of Sapphire and Emerald. The timelines split into two possibilities: the events of FireRed and Sapphire, focusing on Leaf and May, respectively, and the events of LeafGreen and Emerald, focusing on Red and Brendan, respectively. Ultimately, the canon turn of events follows the LeafGreen/Emerald possibility. Unlike in the CPU, Steel and Dark types are widely known in Kanto. Shortly after the events taking place in Kanto and Hoenn, the story of Pokemon Colosseum takes off, focusing on Pokemon snatcher Wes and his quest to purify Shadow Pokemon in the Orre region.
2005: The events of Pokemon HeartGold and SoulSilver take place, followed concurrently by the events of Diamond and Platinum. The canon turn of events follows the story of Platinum and SoulSilver, with Dawn and Ethan (named Lee) being the heroes of their stories, respectively. The alternate path is that of Diamond and HeartGold, which focus on the stories of Lucas and Lyra, respectively. Both stories take place shortly before the events of Pokemon Battle Revolution, where several unnamed trainers take on the Colosseum Challenge in Poketopia.
2007: The events of Pokemon XD: Gale of Darkness take place, where a young trainer named Michael must capture and purify Shadow Pokemon in the Orre region, as Wes had done five years prior. Additionally, he is tasked with the taxing process of purifying XD001, a Shadow Lugia that once took residence in the Johto region two years prior. After Michael captures XD001, the timeline splits into two canon possibilities. In one timeline, Michael does not succeed in purifying XD001. In this case, the events of Pokemon Black take place, starring Hilda as the heroine (though she is named Touko). If Michael successfully purifies XD001, then the events of Pokemon White will take place, starring Hilbert (Touya) as the hero.
2009: As the split of the timeline continues, either Touya or Touko will succeed in capturing Zekrom or Reshiram, then leave Unova in search of N. Here, the events of Pokemon Black 2 and Pokemon White 2 take place. In Black 2, a young trainer named Nate (called Kyouhei in-game) follows in Touko's footsteps and captures Kyurem and Zekrom, while in Pokemon White 2, a girl named Rosa follows in Touya's footsteps and captures Kyurem and Reshiram. The Pokemon World Tournament opens up in Unova in both timelines, where gym leaders and champions from Kanto, Johto, Hoenn, and Sinnoh take part in the ultimate Pokemon tournament. However, during the tournament, another villainous team stationed in the Kalos region attempts to reawaken legendary Pokemon Xerneas (Black's timeline) or Yveltal (White's timeline). Trainers named Calem (White's timeline) and Serena (Black's timeline) begin their quest to stop Team Flare. However, as the Kalos War never took place in this universe, Mega Evolution and the Fairy type do not exist.

Mega Stones Universe:
The universe that focuses on the games released for 3DS, Wii U, and future Nintendo consoles.
3000 Years Before XY: The events of the Kalos War take place, forcing the giant AZ to build a machine that would drain the life force of every creature in its range. He later used this to revive his beloved Floette, but the Pokemon rejects him, angered that he sacrificed so many lives just to save one. He adapted a very long life span after this event, and the activation of the machine began to draw a large meteor toward the Earth.
2013: The events of Pokemon Origins take place, followed concurrently by Omega Ruby and Alpha Sapphire. Unlike in the PSU, Leaf is not known to exist in this timeline, although this is only due to her absence from Pokemon Origins. Origins follows the original plot of both LeafGreen and RBY, with Mega Evolution involved. Omega Ruby, focusing on the events of Brendan setting out to stop Team Magma, and Alpha Sapphire, focusing on May's efforts to stop Team Aqua, take place during this time. The two different timelines converge during a story known as the Delta Episode, in which Brendan or May meets a mysterious woman named Zinnia, and must awaken Rayquaza in order to stop a meteor from destroying the Hoenn region, and the world. After stopping the meteor, Brendan or May discover various portals spread around Hoenn, left behind by the Pokemon Hoopa. Each portal pulls out a Legendary Pokemon from across time and space. Like in Kanto, the Hoenn trainers discover Mega Evolution, in addition to Primal Reversion. However, it is unknown if these methods of evolution are ever discovered in other regions.
2013-2018: The stories of the Orre region, Johto, Sinnoh, and Unova take place, and the events transpire the same way they do in Pokemon Generations, with slight differences. Though the "Generations" logo is taken from the anime on YouTube, this timeline represents my ideas for Pokemon remakes, notably Colosseum HD, Gale of Darkness HD, Temporal Diamond/Celestial Pearl, Pitch Black/Radiant White, and Battle Revolution 2/Stadium 3.
2020: The events of Pokemon X and Pokemon Y take place, where Serena or Calem, respectively, must stop Lysandre and Team Flare from reviving Xerneas or Yveltal and reactivating the ancient machine that eradicated many human and Pokemon lives 3000 years ago. On the other side of the world, trainers Nate and Rosa unite with Pokemon Trainer N in order to stop Ghetsis and a revived Team Plasma from taking over the Unova region with Kyurem. Afterwards, a Pokemon World Tournament takes place that invites gym leaders and champions from Kanto, Johto, Hoenn, and Sinnoh to participate.
2021: A new form of Pokemon battles is discovered in the Ferrum region, and that gives birth to the Pokken Tournament. The events of Pokken Tournament take place, and a mysterious Pokemon known as Shadow Mewtwo enters the stage.
2023: The events of my Pokemon game idea, Pokemon Legends, take place. A former member of Cipher named Victor seeks to capture Dialga, convert it into a Shadow Pokemon, and capture every known Pokemon trainer and Legendary Pokemon throughout history, and form a Syndicate from the fallen ranks of Teams Rocket, Magma, Aqua, Galactic, Plasma, and Flare. Zinnia and N meet up with a Celebi, who informs N of the plot, and the two travel to the Orre region to find a trainer with the skills to take down Shadow Pokemon. With Wes and Michael unable to assist them, the two meet a former Pokemon researcher named Vincent, who has taken up Pokemon training in order to study Mega Evolution and Primal Reversion. With Celebi and his own Blaziken by his side, and armed with Wes' Snag Machine and Michael's Aura Reader, Vince prepares to transcend Pokemon history in order to stop Victor's nefarious plot.
Sometime after 2024: This is where Pokemon Sun and Moon fall. Since Red and Green (Blue) were shown in a trailer to be much older than in previous games, we can assume that Sun and Moon take place at least 10 years after Omega Ruby and Alpha Sapphire. However, whether the two are in their 20's or their 30's has yet to be announced, so at the least, I'm placing the events as taking place at least one year after Pokemon Legends, since Sun and Moon did not exist at the time the concept was created, and most games take place at least a year apart.
After the events of Sun and Moon pass, the trainers Sun and Moon fall through an Ultra Wormhole into the world of Pokemon Legends, where they meet Vincent Harmonia in a DLC epilogue to the main story. They engage in a friendly battle with Vincent before returning to their own world(s).

Pokemon Dimensions:
In quoting Sun and Moon's initial tagline, "This is where it all comes together!". Set roughly a month after the epilogue of Pokemon Legends, wherein he faced Sun and Moon in a Pokemon battle, the story of Vincent is about to come to a close until he meets a new trainer calling himself Valen. When he is challenged by Valen, he is faced against not only Hoopa Unbound, but several strange Pokemon he's never seen before, which Valen refers to as "Ultra Beasts". Before he can utilize Mewtwo and Blaziken's Mega Evolution, Vincent himself is hit by an attack from one of the creatures, separating himself from Mewtwo and Celebi. With only Blaziken by his side, Vincent wakes up in a tropical region, where he meets a young girl named Selene, who has just begun her Pokemon journey. With a hazy recollection of what recently happened, Vincent asks Selene to take him to her region's champion. When he meets the champion, he discovers that it is Sun, however, he has aged 8 years since the last time they met...
The premise of Pokemon Dimensions is that it is a sequel to Pokemon Legends. Since the protagonist of Legends suffers from memory loss after falling through an Ultra Wormhole, players would take the role of a new hero to help guide the prequel's protagonist through a journey that sees them travel through different Pokemon worlds, rather than jumping through timelines. As such, this game would truly be where all three timelines come together, as Selene would team up with a shiny Giratina in her quest to stop Valen from using the Ultra Beasts to destroy the Pokemon Universe. This game technically takes place 9 years and one month after the events of Pokemon Legends, and 8 years after the events of Pokemon Sun and Moon, however, since it isn't tied to a single dimension, it doesn't take place during a single time period. As the three timelines take place in different dimensions, the player could travel to the Monochrome timeline during the events of Gold and Silver, yet find themselves in the Mega Stones universe during the events of Omega Ruby and Alpha Sapphire.

NOTE:
Previously, I had a section dedicated to the real world, which was set in real-time 2016 in comparison to the Monochrome Timeline. This world still exists in The Crossover Game, and represents games like Hey You, Pikachu! and Pokemon GO, however, it isn't included in Pokemon Dimensions. Additionally, the anime timeline would also crossover into Pokemon Dimensions, with Ash Ketchum being based off of his appearance in Pokemon XY, though his Kanto, Johto, Hoenn, Sinnoh, Unova, and Alola variations would also make an appearance. Since the Pokemon anime is basically its own universe and time never seems to flow normally in it, it isn't included on this image.

Description
The Pokemon Timeline in The Crossover Game is divided into three universes. Although events in each universe take place simultaneously, the time placement in each universe is different, reflecting on the year that the first game of each rebooted Generation was released in Japan. (Generation I timeline begins in 1996, Generation III timeline begins in 2002, and Generation VI timeline begins in 2013).
You may curious as to the reasoning behind the different timeline placements. This is simply an in-game explanation for why some games, though they follow the same plot, seem to be more technologically advanced than their counterparts. (Such as Red/Blue having primitive PC storage boxes, FireRed/LeafGreen needing to link a supercomputer in order to trade with Hoenn games, and Omega Ruby/Alpha Sapphire supporting Wonder Trading and advanced PC storage boxes, among other tech).
Despite the different placements in time, each universe follows a simultaneous history, though there are key differences in each universe. The three universes are referred to as the "Classic Pokemon Universe" (or "CPU", also known as "Monochrome Universe"), the Pokemon Shared Universe (shortened to "PSU"), and the "Mega Stones Universe" (shortened to "MSU"). There is a fourth universe known as the Real World, which is based on the real world and as such, Pokemon is just a series of video games that began in 1996 and continues to the modern day.
Note: If a Pokemon game is missing from this list, such as Silver Version or Pokemon Pearl, it is because I don't own that game or have plans to buy it. The canon within The Crossover Game reflects on my video game collection and the games I plan to buy or have played before. Additionally, if some of the story elements I list don't match up with the actual games or if some games follow a different order than you'd expect them to, keep in mind that this is a fanfiction, and does not reflect entirely on the official Pokemon canon.

Classic Pokemon Universe (Monochrome):
This universe reflects on the Pokemon games released for the Game Boy, Game Boy Color, and Nintendo 64.
1996: The plots of Pokemon Red, Blue, and Yellow take place around the same time as Pokemon Stadium. The Mewtwo that appeared in Pokemon Stadium is the same Mewtwo that is later captured by Red. Unlike most alternate timelines, Red, Blue, and Yellow's storylines all follow virtually identical plots, with the only differences being Red's choice of Pokemon in his party, and Yellow's alternate storytelling (Pikachu starter, fighting Jesse and James, etc.)

1999: The plots of Pokemon Gold and Crystal take place at the same time as Pokemon Stadium 2. Here is where the timeline splits, even though both stories follow the same overall theme. In the Pokemon Gold timeline, Gold is the hero of the story, while the Pokemon Crystal timeline focuses on Kris becoming the heroine. Both stories end with a battle against Red on Mt. Silver. The events in Johto also lead to the discovery of Steel and Dark type Pokemon, and these Pokemon later migrate to Kanto.

Post-1999: Since no future Pokemon games are able to connect to Generations I and II (excluding Pokemon Bank with the 3DS versions of RBY), the story of this Pokemon world is cut short, and it is believed that the other regions and 500+ species of Pokemon simply don't exist in this universe. This reflects on Nintendo's original plans to end the Pokemon series after Gold and Silver.

Pokemon Shared Universe:
This universe reflects on the games released for the Game Boy Advance, GameCube, Nintendo DS, and Nintendo Wii.
2002: The events of Pokemon FireRed and LeafGreen take place, followed concurrently by the events of Sapphire and Emerald. The timelines split into two possibilities: the events of FireRed and Sapphire, focusing on Leaf and May, respectively, and the events of LeafGreen and Emerald, focusing on Red and Brendan, respectively. Ultimately, the canon turn of events follows the LeafGreen/Emerald possibility. Unlike in the CPU, Steel and Dark types are widely known in Kanto. Shortly after the events taking place in Kanto and Hoenn, the story of Pokemon Colosseum takes off, focusing on Pokemon snatcher Wes and his quest to purify Shadow Pokemon in the Orre region.
2005: The events of Pokemon HeartGold and SoulSilver take place, followed concurrently by the events of Diamond and Platinum. The canon turn of events follows the story of Platinum and SoulSilver, with Dawn and Ethan (named Lee) being the heroes of their stories, respectively. The alternate path is that of Diamond and HeartGold, which focus on the stories of Lucas and Lyra, respectively. Both stories take place shortly before the events of Pokemon Battle Revolution, where several unnamed trainers take on the Colosseum Challenge in Poketopia.
2007: The events of Pokemon XD: Gale of Darkness take place, where a young trainer named Michael must capture and purify Shadow Pokemon in the Orre region, as Wes had done five years prior. Additionally, he is tasked with the taxing process of purifying XD001, a Shadow Lugia that once took residence in the Johto region two years prior. After Michael captures XD001, the timeline splits into two canon possibilities. In one timeline, Michael does not succeed in purifying XD001. In this case, the events of Pokemon Black take place, starring Hilda as the heroine (though she is named Touko). If Michael successfully purifies XD001, then the events of Pokemon White will take place, starring Hilbert (Touya) as the hero.
2009: As the split of the timeline continues, either Touya or Touko will succeed in capturing Zekrom or Reshiram, then leave Unova in search of N. Here, the events of Pokemon Black 2 and Pokemon White 2 take place. In Black 2, a young trainer named Nate (called Kyouhei in-game) follows in Touko's footsteps and captures Kyurem and Zekrom, while in Pokemon White 2, a girl named Rosa follows in Touya's footsteps and captures Kyurem and Reshiram. The Pokemon World Tournament opens up in Unova in both timelines, where gym leaders and champions from Kanto, Johto, Hoenn, and Sinnoh take part in the ultimate Pokemon tournament. However, during the tournament, another villainous team stationed in the Kalos region attempts to reawaken legendary Pokemon Xerneas (Black's timeline) or Yveltal (White's timeline). Trainers named Calem (White's timeline) and Serena (Black's timeline) begin their quest to stop Team Flare. However, as the Kalos War never took place in this universe, Mega Evolution and the Fairy type do not exist.

Mega Stones Universe:
The universe that focuses on the games released for 3DS, Wii U, and future Nintendo consoles.
3000 Years Before XY: The events of the Kalos War take place, forcing the giant AZ to build a machine that would drain the life force of every creature in its range. He later used this to revive his beloved Floette, but the Pokemon rejects him, angered that he sacrificed so many lives just to save one. He adapted a very long life span after this event, and the activation of the machine began to draw a large meteor toward the Earth.
2013: The events of Pokemon Origins take place, followed concurrently by Omega Ruby and Alpha Sapphire. Unlike in the PSU, Leaf is not known to exist in this timeline, although this is only due to her absence from Pokemon Origins. Origins follows the original plot of both LeafGreen and RBY, with Mega Evolution involved. Omega Ruby, focusing on the events of Brendan setting out to stop Team Magma, and Alpha Sapphire, focusing on May's efforts to stop Team Aqua, take place during this time. The two different timelines converge during a story known as the Delta Episode, in which Brendan or May meets a mysterious woman named Zinnia, and must awaken Rayquaza in order to stop a meteor from destroying the Hoenn region, and the world. After stopping the meteor, Brendan or May discover various portals spread around Hoenn, left behind by the Pokemon Hoopa. Each portal pulls out a Legendary Pokemon from across time and space. Like in Kanto, the Hoenn trainers discover Mega Evolution, in addition to Primal Reversion. However, it is unknown if these methods of evolution are ever discovered in other regions.
2013-2018: The stories of the Orre region, Johto, Sinnoh, and Unova take place, and the events transpire the same way they do in Pokemon Generations, with slight differences. Though the "Generations" logo is taken from the anime on YouTube, this timeline represents my ideas for Pokemon remakes, notably Colosseum HD, Gale of Darkness HD, Temporal Diamond/Celestial Pearl, Pitch Black/Radiant White, and Battle Revolution 2/Stadium 3.
2020: The events of Pokemon X and Pokemon Y take place, where Serena or Calem, respectively, must stop Lysandre and Team Flare from reviving Xerneas or Yveltal and reactivating the ancient machine that eradicated many human and Pokemon lives 3000 years ago. On the other side of the world, trainers Nate and Rosa unite with Pokemon Trainer N in order to stop Ghetsis and a revived Team Plasma from taking over the Unova region with Kyurem. Afterwards, a Pokemon World Tournament takes place that invites gym leaders and champions from Kanto, Johto, Hoenn, and Sinnoh to participate.
2021: A new form of Pokemon battles is discovered in the Ferrum region, and that gives birth to the Pokken Tournament. The events of Pokken Tournament take place, and a mysterious Pokemon known as Shadow Mewtwo enters the stage.
2023: The events of my Pokemon game idea, Pokemon Legends, take place. A former member of Cipher named Victor seeks to capture Dialga, convert it into a Shadow Pokemon, and capture every known Pokemon trainer and Legendary Pokemon throughout history, and form a Syndicate from the fallen ranks of Teams Rocket, Magma, Aqua, Galactic, Plasma, and Flare. Zinnia and N meet up with a Celebi, who informs N of the plot, and the two travel to the Orre region to find a trainer with the skills to take down Shadow Pokemon. With Wes and Michael unable to assist them, the two meet a former Pokemon researcher named Vincent, who has taken up Pokemon training in order to study Mega Evolution and Primal Reversion. With Celebi and his own Blaziken by his side, and armed with Wes' Snag Machine and Michael's Aura Reader, Vince prepares to transcend Pokemon history in order to stop Victor's nefarious plot.
Sometime after 2024: This is where Pokemon Sun and Moon fall. Since Red and Green (Blue) were shown in a trailer to be much older than in previous games, we can assume that Sun and Moon take place at least 10 years after Omega Ruby and Alpha Sapphire. However, whether the two are in their 20's or their 30's has yet to be announced, so at the least, I'm placing the events as taking place at least one year after Pokemon Legends, since Sun and Moon did not exist at the time the concept was created, and most games take place at least a year apart.
After the events of Sun and Moon pass, the trainers Sun and Moon fall through an Ultra Wormhole into the world of Pokemon Legends, where they meet Vincent Harmonia in a DLC epilogue to the main story. They engage in a friendly battle with Vincent before returning to their own world(s).

Pokemon Dimensions:
In quoting Sun and Moon's initial tagline, "This is where it all comes together!". Set roughly a month after the epilogue of Pokemon Legends, wherein he faced Sun and Moon in a Pokemon battle, the story of Vincent is about to come to a close until he meets a new trainer calling himself Valen. When he is challenged by Valen, he is faced against not only Hoopa Unbound, but several strange Pokemon he's never seen before, which Valen refers to as "Ultra Beasts". Before he can utilize Mewtwo and Blaziken's Mega Evolution, Vincent himself is hit by an attack from one of the creatures, separating himself from Mewtwo and Celebi. With only Blaziken by his side, Vincent wakes up in a tropical region, where he meets a young girl named Selene, who has just begun her Pokemon journey. With a hazy recollection of what recently happened, Vincent asks Selene to take him to her region's champion. When he meets the champion, he discovers that it is Sun, however, he has aged 8 years since the last time they met...
The premise of Pokemon Dimensions is that it is a sequel to Pokemon Legends. Since the protagonist of Legends suffers from memory loss after falling through an Ultra Wormhole, players would take the role of a new hero to help guide the prequel's protagonist through a journey that sees them travel through different Pokemon worlds, rather than jumping through timelines. As such, this game would truly be where all three timelines come together, as Selene would team up with a shiny Giratina in her quest to stop Valen from using the Ultra Beasts to destroy the Pokemon Universe. This game technically takes place 9 years and one month after the events of Pokemon Legends, and 8 years after the events of Pokemon Sun and Moon, however, since it isn't tied to a single dimension, it doesn't take place during a single time period. As the three timelines take place in different dimensions, the player could travel to the Monochrome timeline during the events of Gold and Silver, yet find themselves in the Mega Stones universe during the events of Omega Ruby and Alpha Sapphire.

NOTE:
Previously, I had a section dedicated to the real world, which was set in real-time 2016 in comparison to the Monochrome Timeline. This world still exists in The Crossover Game, and represents games like Hey You, Pikachu! and Pokemon GO, however, it isn't included in Pokemon Dimensions. Additionally, the anime timeline would also crossover into Pokemon Dimensions, with Ash Ketchum being based off of his appearance in Pokemon XY, though his Kanto, Johto, Hoenn, Sinnoh, Unova, and Alola variations would also make an appearance. Since the Pokemon anime is basically its own universe and time never seems to flow normally in it, it isn't included on this image.