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The Rise of Team Flare- The Kalos Champion
Shortly after the player arrives in Kalos, he/she finds three people waiting. They introduce themselves as Trevor, Tierno, and Calem (If the player is female)/Serena (If the player is male), Pokemon Trainers from Kalos. They encourage the player to meet Professor Sycamore again, but this time in the Pokemon Lab in Lumoise City. The player also meets his/her brother again, who gives the player a free Charmander/Squirtle/Bulbasaur he breeded.
In the lab, the Professor congratulates the player and gives him/her a Poke Radar along with the National Pokedex. The Professor also tells the player that the Kalos region also has a Pokemon League and challenges the player to defeat the Champion. However, the Professor recieves strange radio signals somewhere in the west side of the region, asking the player and Calem/Serena to investigate. When they get there, the two discover that the signals are coming from Geohenge Town and head over to see what's going on.
At Geohenge Town, the two are shocked to discover the giant hole in the middle of the town opened. Calem/Serena tells the player about the ultimate weapon Team Flare activated three years ago before the two carefully head down into a secret facility, or the Ruined Team Flare HQ.
In the HQ, the player and Calem/Serena spilt up to find out what's going on. The player finds a strange room that is still somewhat covered in rubble. Xerosic then arrives and explains that a man named Lysandre tried to use the weapon but is still trapped. The two fight once more before Calem/Serena runs into the room. Xerosic then activates a machine that clears the rubble. A man then climbs out of a hole, revealing himself to be Lysandre. Lysandre challenges the player to a fight, and Lysandre loses. The two villains manage to escape before AZ enters the room, saying that he was the one responsible for the ultimate weapon and apologizes before the three exit the HQ.
After the player has won all eight Kalos Gym Badges, Lysandre makes a public announcement on the Holo Caster saying that he will use Xerneas' and Yveltal's power to eliminate "the filith of this world". The Professor traces Lysandre's location to the Legendary Peaks, a place where Xerneas and Yveltal were said to be born according to Kalos myths. After arriving to the top of the peak, Lysandre and Xerosic are seen summoning Xerneas and Yveltal. Xerosic notices the player and holds them off, but is ultimatly defeated. However, it is too late, as the two Legendary Pokemon are by Lysandre's side. Luckily for the player, Trevor, Tierno, Calem, Serena, and AZ arrive to help. Unfornatly, Lysandre creates a mystical barrier behind the player, eliminating any help.
After one final battle between Lysandre and the player, Calem (if the player is male)/Serena (if the player is female) is the first to notice the barrier is broken and approces Lysandre. The villian, in a desperate effort, attempts to use Xerneas and Yveltal, but their power backfires, warping Lysandre into an alternate dimension. Xerneas and Yveltal flee, leaving the six alone in the peaks. Xerosic then turns himself in, saying that there's nothing left for him to do.
After the player has defeated the Elite Four, Calem (if male)/Serena (if female) reveals him/herself to be the Kalos Champion. After one last fight, the player becomes the Kalos Champion as well as the Ampardo Champion. The Professor invites the player to a parade, just like Calem/Serena. With that, the game's story finally ends.
Legendary Nightmare- A Girl's Deepest Fears
If the player goes to the Berry Farm south of Route 7, he or she will find the old farmer's grandaughter stuck in a nightmare in a house. The player has to find a Psycho Crystal to travel inside the girl's mind to stop the nightmare. Inside the girl's mind is a mansion haunted by all kinds of strange creatures (Similar to Pokestar Studio props) that cannot be caught. In the basement of the mansion is Darkrai, the Pokemon responsible for the girl's suffering. When sighted, the player is teleported out of the dream as the girl wakes up. The TV suddently turns on, saying a mysterious Pokemon has been sighted in the Sea Spirit's Den.
When the player arrives in the Den, Darkrai is waiting. It tries to trap the player in a nightmare, but the Psycho Crystal prevents it. Darkrai then battles the player, but is caught by him/her.
If the player goes back to the Berry Farm, the farmer gives the player a large amount of money, thanking him/her for their troubles.
Genesect- The Genetic Insect
When the player vists the Ampardo News Station, a reporter named Alexi is scearching for a Pokemon named Genesect. Genesect was last seen roaming Ampardo before the player arrived. After encountering Genesect in the wild, it escapes to an underground cave. Alexi and the player travel through the cave to find the Lost City, a place described in legends.
After discovering Genesect in the ancient Throne Room, the player captures Genesect and Alexi returns to Kalos.
Traveling Through Time- Celebi and Lysandre
After defeating Lysandre, the player can travel back to their hometown to find Celebi. After following it to the new Ancient Shrine, it can be caught. If the player returns to the shrine with Celebi, it will allow them to travel back in time. There, they see Lysandre as a young child, being kicked out of his home by his parents. Lysandre only has a Magikarp with him, and vows to make his parents proud of him. He travels to the Pokemon League, hoping to get accepted in as a challenger, but is laughed out by the Victory Road trainers. Lysandre then leaves, catching a Litleo with the only thing he was able to buy on his own, a Pokeball. He trains up, catching a Murkrow on the way, challenging the eight Gym Leaders. Years later, he finally arrives back to Victory Road and manages to make it to the Pokemon League, but loses to the Elite Four.
Lysandre arrives back home, hoping to see his parents waiting for him, but they are gone from his home. There, he gains his twisted vision that the world is evil, now promising to himself that he will let others see the pain he went through. He leaves, and Celebi takes the player back to their own time.
The Drifting Ship- A Spirit from the Sea (Event)
If the player goes to the Grand Harbor, he or she will find a special news boat about to leave. The captain, sensing danger, invites the player to join them on a trip to a special island. However, the boat breaks down in the middle of the ocean. Luckily, a cruise ship drifts by as the player and the news crew board the cruise. When they go inside, they find it completely empty.
After exploring, the player notices the news crew is missing. The player follows laughing to the captain's quarters, where Hallowpump is with the news crew, trapping them in vines. After a battle, Hallowpump is captured by the player. The news crew go back to their boat, where it begins to work again. The captain decides to go back the Ampardo, and the news report is cancelled.
When the player goes to the Kalos Pokemon League again, a messenger appears, giving a letter to the player. The letter gives the player directions to a new area in the Winding Woods. When the player arrives, a man in white robes walks in, giving the player a purple flute, instructing the player to play it at the highest mountain in Ampardo. When played at the Legendary Peaks, a transparent staircase appears, leading up to a glass platform. When the player stands on the platform, a portal appears, and a voice tells the player to jump in.
Inside, the player finds him/herself in the Distortion World. After navigating through the dimension, Giratina appears, and is caught by the player. The man in white robes appears again, giving the player the three orbs related to the Creation Trio, taking back the flute. A white light flashes, and the player is back in his/her hometown. The white robed man is never seen again.