List of Changes and Additions to Games and How They Effect the Series


Kanto

Madame Boss of Team Rocket hires a science team from Genesis Biocorp to run experiments on rare pokemon, including Lasuno and Larisa.
Team Rocket abandons Lasuno and Larisa in the Moonstone Mountains in 1990 and the scientist is tasked with researching the whereabouts of a Mew afterwards.
Madame Boss launches an expedition to locate a Mew in 1991 but it comes to a dead end with no more than minor traces in the mountains far north of Kanto.
Madame Boss passes and Giovanni takes over Team Rocket in 1995. He picks up after his mother’s work and launches a second expedition to locate Mew, finding a DNA sample in the mountains near Rota.
Giovanni cuts ties with Genesis Biocorp and hires a team led by Dr. Fuji, including Blaine, to clone Mew with the DNA sample. The result is Mewtwo, who goes rogue and destroys the facility in Cinnabar, then flees to Cerulean Cave.
Dr. Fuji is decommissioned and retires in Lavender after the incident. Blaine returns to the Cinnabar gym.
Red selects Charmander as his starter. Blue selects Squirtle. They start their journey in 1996.
While passing through Viridian, Red catches a glimpse of a flaming bird flying over Mt. Indigo west of the city. Unknowingly, this is Nirehtra the Moltres.
Red learns of the cave near Cerulean and rumors surrounding a powerful pokemon supposedly living there.
On the way to Rock Tunnel, Red encounters Telestro the Zapdos near an abandoned power plant, who appears disturbed by something and doesn’t notice Red.
Giovanni questions Dr. Fuji in Lavender’s Pokemon Tower about the whereabouts of Mewtwo and leaves as Red shows up, leaving him to deal with Team Rocket grunts.
While infiltrating the Rocket hideout in Celedon, Red gets hints of Giovanni’s motives to go after Mewtwo, but doesn’t yet learn of the pokemon’s identity.
Red is unable to stop Giovanni from taking the master ball from Silph Co. and Team Rocket gets away, leaving the top of the building destroyed.
On the way to Cinnabar from Fuschia, Red encounters Felana the Articuno at the Seafoam Islands, who promptly leaves towards the north.
While exploring the burned mansion in Cinnabar, Red finds records of Team Rocket’s work to clone Mew, and the creation of Mewtwo. He battles Blaine, who learns of Giovanni’s plans to recapture Mewtwo.
After being defeated in Viridian gym, Giovanni leaves to go after Mewtwo, having used the gym battle as a distraction for Team Rocket to prepare for the mission.
Blaine contacts Red and has him go to the Moonstone Mountains to explore an old facility near them, just outside Kanto. They come across reports of their experiments on pokemon, including Lasuno and Larisa, and learn the location of Mewtwo.
Blaine contacts the other gym leaders to go to Cerulean Cave and help face Team Rocket. Once they arrive, the organization is guarding the cave and they fight through them to Giovanni, who has found Mewtwo. He shortly captures it in the master ball and fights through Red and the gym leaders, escaping the cave.
Mewtwo breaks out of the master ball, attacks Team Rocket, and flees to the Moonstone Mountains, where it is attacked by Nirehtra, Telestro and Felana. Once Red arrives, the three birds are downed and he faces Mewtwo, defeating it and driving it away, having calmed its rage. Giovanni approaches Red and formally disbands Team Rocket, then leaves.
Red faces Blue in the Indigo League and becomes Champion. Blue takes over leadership of the Viridian gym.
Red explores the Sevii Islands and takes out the remnants of Team Rocket, then heads to Johto to become stronger, coming across Giovanni arguing with a red-haired kid about his plans.

Hoenn

Brendan moves from Olivine to Littleroot and starts his journey in 1996 with Treecko, and May with Torchic.
Brendan faces both Team Magma and Aqua, who awaken Groudon in Mt. Chimney and Kyogre in Seafloor Cavern. The two enter Primal Reversion in Sootopolis but are stopped by Brendan and May, thwarting Zinnia’s original plan to summon Rayquaza.
May quits her journey to help Professor Birch with his field research and Brendan becomes champion of the Ever Grande League.
While investigating the meteor in 1997, Brendan learns of the Draconids, Hoenn’s history, and the foundation of the two nearby countries Chora and Nero, who worship Groudon and Kyogre respectively.
Brendan faces Rayquaza atop Sky Pillar and helps him achieve his Mega Evolution. They destroy the meteor and battle Deoxys. Upon being defeated, Deoxys’s core gem falls into the ocean. Rayquaza returns to the sky and Brendan goes to the Battle Resort to hone his skills.
Gabby and Ty of Mauville News get into Mossdeep’s space station and leak the news of Deoxys’s appearance to the press. Genesis Biocorp sends a team to search for the remaining core in the ocean south of Hoenn in 2000, collecting it and taking it to their base in Opelucid.

Orre

After defeating Cipher atop Realgem Tower in 1997, Wes and the Orre police spot Ho-Oh flying over the tower towards the east, where it heads back towards Johto to the Bell Tower in Ekruteke.

Johto

Red collects the Johto badges in 1998 and heads into the Silver Mountains to continue training.
Ethan starts his journey in 1999 with Cyndaquil and encounters Kamon, who steals a Totodile from Professor Elm.
Ethan witnesses Entei, Raikou and Suicune fleeing the Brass Tower in Ekruteke and comes across Eusine, who is on a hunt for Suicune.
After getting the Olivine gym badge, Ethan encounters Suicune in Ekruteke, who leads him to the Bell Tower and faces him inside. After the battle, Suicune runs off and the monks inside tell Ethan he’s destined for greatness.
While traveling through Mt. Mortar, Ethan comes across an old mansion and finds Lokoko the Ninetales. After learning of her past, he calms her down of her anger and frees her from the mansion by destroying her old pokeball. Lokoko wanders away into the mountains.
On the way to the Ice Path, Ethan is caught up in Team Rocket’s attempt to capture Raikou. After fighting them off with unexpected help from Lokoko, he faces Raikou, who afterwards flees. Lokoko leaves as well without a word.
After defeating Clair in the Blackthorn gym, Ethan comes across Chrissa and Samuel, who are visiting from Pallet with Aerthos the Dragonite and Sierra the Flygon. They tell him what Kanto’s like and advise him to visit there someday.
While traveling through Mt. Indigo, Ethan comes across Entei, who faces him in battle. Lokoko appears again to face Entei. Afterwards, Entei flees and Lokoko leaves again, having apparently grown fond of Ethan. Ethan challenges the Indigo League, becoming champion.
Ethan visits Ekruteke on request by Morty to go to the Bell Tower. After having been acknowledged by the three legendary beasts, Ethan gains passage to the top of the tower, where he faces Ho-Oh. After the battle, Ho-Oh leaves him with a sacred ash.
On the way to Olivine, Ethan encounters Lokoko again, who challenges him to battle, before joining him.
Ethan heads to Kanto via the S.S. Aqua in 2000 and collects the eight gym badges. He gets news of a powerful trainer who defeated Team Rocket here before while traveling through the region.
Ethan defeats a Team Rocket grunt in Cerulean, who later leaves to Unova to retire and start a family in Icarus.
After being defeated on Mt. Silver by Ethan, Red wanders off to explore other regions and become stronger once again.
Ethan goes to Whirl Islands after reports of a mysterious organization appearing there. He fails to stop them from capturing a Lugia there, and its son, Licentia, flees the scene to search for them.

Sinnoh

Dawn starts her journey with Piplup in 1999 with Barry, who picks Turtwig.
Dawn learns of Palkia’s appearance atop Spear Pillar. Cyrus uses the Red Chain to trap Palkia, luring Dialga from the Flare Continent and trapping him as well.
Giratina appears from the Reverse World and captures Cyrus. Dawn and Cynthia go in after them and face Giratina, who then wanders off with Cyrus.
Dawn faces the Sinnoh League and becomes champion.
Cyrus has been reported by Team Galactic remnants to have disappeared from the Reverse World. When Dawn meets Giratina in Turnback Cave, she learns Cyrus was killed by a force called Chaos in a distant part of the Reverse World, brought about by something from another realm hundreds of years ago. Team Galactic effectively disbands after this.

Orre

Michael sets out across Orre to purify Shadow pokemon in 2002. His Eevee evolves into an Umbreon in Gateon Port.
Michael meets Licentia the Lugia at Gateon Port after returning from exploring the abandoned S.S. Libra. Licentia was injured and a medical team by Professor Krane helps him recover. He apparently arrived from Johto in search of something, but was hurt when approaching Citadark Isle due to the weather conditions.
After finding out Cipher’s location at Citadark Isle, Michael goes there after Licentia suddenly leaves to confront them.
With Licentia’s help, Michael defeats Cipher’s boss Greevil and Shadow Lugia is taken in for purification. The process, however, proves difficult and heavily strains Lugia. After being attacked by Miror B, who has Cipher’s last Shadow pokemon Dragonite, Lugia finally manages to break from Shadow, but dies shortly after, leaving Licentia an orphan.
Licentia leaves Orre to search for comfort elsewhere after the loss of his father. Michael eventually purifies all the Shadow pokemon and the Cipher Key Lair is decommissioned and placed under watch by the local authorities.

Unova

Hilbert starts his journey with Tepig in 2004. His friends Cheren and Bianca pick Oshawott and Snivy respectively.
Hilbert eventually meets Reshiram atop Dragonspiral Tower, along with a family of Ninetales: Serenity, Cerathinas and Esira. Reshiram chooses to go with Hilbert, leaving the three Ninetales to watch the tower while he’s away.
While Hilbert is confronting N in Team Plasma’s castle, Reshiram appears to face Zekrom. After the battle, and Ghetsis is defeated, N leaves the castle with Zekrom to pursue his ideal. Reshiram returns to Dragonspiral Tower.
Cheren visits Black City and learns of the high crime rate in the city. He encounters Eclisse the Espeon briefly and later decides to become a gym leader to help better the region.
Hilbert challenges the Unova League and becomes champion.
A landslide in the mountains north of Opelucid renders the Unova League inaccessible in 2005. A new path is built from Humilau and the League is restored.
Nate starts his journey with Snivy in 2006, and his friend Hugh picks Tepig.
Nate faces Neo Team Plasma in Opelucid and deals with the Shadow Triad. Drayden tries to keep the DNA Splicers from them before the city is frozen over by the Plasma Frigate. The impact of the event reaches all the way to Black City, where Eclisse and her son Umbros live. Many survivors from Opelucid move to Black City as refugees.
Nate faces Ghetsis in the Giant Chasm, controlling Kyurem. N appears with Zekrom to try and stop him, but the two fuse with the use of the DNA Splicers, forcing Nate to fight them himself. After the battle, the two split and Kyurem retreats deeper into the cave, with Ghetsis defeated and Neo Team Plasma disbanded.
Nate faces N in his castle with Zekrom. After the battle, Zekrom leaves N, who chooses to find a new path in his life.
Nate challenges the Unova League and becomes champion.
Nate later visits Black City, learning of the city’s state after Opelucid was frozen. After challenging Black Tower, he leaves Unova to try and become a better trainer.
The ice in Opelucid melts with the Summer warmth later in 2006.

Kalos

Calem starts his journey with Chespin in 2006. His friends, Serena and Shauna pick Fennekin and Froakie respectively.
Serena decides to pursue Pokemon Showcases instead of challenging gyms.
Calem faces Team Flare in Geosenge and follows them into their lab under the town. Lysandre tries to set off the Kalos Weapon but Yveltal awakens and attacks him, forcing the weapon to backfire on itself and destroying it. Yveltal flees the lab to Liathear, leaving traces of the passage behind, buried under the rubble.
Serena leaves to Hoenn to take on Pokemon Contests with her Braixen after being defeated by the Kalos Queen Aria in the Pokemon Showcase.

Alola

Red and Blue are called to Alola in 2006 to run the Battle Tree as two of the world’s strongest trainers.
Selene starts her journey with Popplio after moving to Melemele Island from Viridian in 2006. Her friend Hau picks Litten.
Selene faces Team Skull and the Aether Foundation until Lillie’s Cosmog Nebby evolves into Lunala and helps to stop them.
After the Aether Foundation is defeated, Selene challenges the newly formed Alola League and becomes the first champion.
Lillie and her mother Lusamime leave to Kanto to try and find help for Lusamime’s sickness after her symbiosis with Nihelego. They seek help from Bill due to his work with the pokemon transfer system that temporarily fused him with a Rattata.
Selene challenges the Battle Tree run by Red and Blue and defeats them.