The game starts in Adventurst Town in the player's room, which starts a cutscene showing the player with the evolved forms of all the Intimas starters, and catching a bunch of Pokemon. The player wakes up, and gets dressed (The plater chooses what they wear), and eventually visits Professor Pine in his lab, where the player chooses one of the three starter Pokemon, Laproise, Heasle, or Seedling. After the selection, Professor Pine requests a battle, and uses the starter Pokemon with the type disadvantage. No matter the result of the battle, the Professor gives the player their own Pokedex, and five Pokeballs, and the player starts off on their journey.
Right before exiting Adventurst Town, you come across two men using their Pokemon to fight against a young boy. The player fights against the thugs, and two shadowy figures assist you. The men run away, and the shadowy figures are revealed to by your two neighbors, Daphne and Zeke. It is revealed that the player is part of Team Silence. The other members take you underneath a bridge, and inform you that they are wanted by the police. The meeting is cut short when they hear someone nearby, and the player continues with their quest.
The player enters Route 1, and eventually comes across a ghost-like figure resembling Gracie, the Resperto Gym Leader. After she finishes speaking, she disappears and a Growth Berry is found on the ground. The player battles all the trainers in the route, and eventually enters Resperto City, where his newely introduced twin brother or sister depending on the player's gender, battles the player. After the player wins, they continue on with their journey.
Over the course of their journey, the player will have numerous encounters with the other members of Team Silence, and eventually the Team is discovered by the player's sibling, and eventually the sibling joins. The plot comes to a head, sometime after the 9th Gym, when the player and Team Silence are transported to the Spirit World. They player and Team Silence try escaping, but evenutally everyone in Team Silence gets their life force absorbed, thus becoming ghosts. The player hides, and finds Gracie's human body, and the player eventually defeats some of the ghosts, but the rest all escape to the human world. The player comes across the whole Intimas League and Elite Four battling the ghosts, and the day is saved when the the Intimas Champion teams up with Gracie and the Player to defeat the rest.
From then on, the player continues its Intimas journey, and defeats the final two gyms. With another Team Silence encounter, Daphne informs the player about the Elite Five, and the player heads off to Libertas City. Once the player gets there, they battle the Elite Four, and enters the hall of Champions, and finds out that the Champion is absent. Terrence sends the player Inviron Town to look for Vincent. The player finds Vincent in the Botanical Garden, admiring the nature. The player convinces Vincent to return as his duty of Champion, and the player must defeat the Elite Five again, and finally beat the champion. Vincent leads the player to a secret room in the Hall of Champions, as the player and their Pokemon are added.
After the main plot of the game has been completed, many inaccessible parts of Intimas, such as the Intimas Islands, will be unlocked. When the player returns to Adventurst Town, the whole town throws them a party for becoming the Champion. The player's mother gives the player several new clothes, and the player leaves to find the rest of Team Silence. The player finds them in an alley, being arrested for stealing Pokemon, when they were actually returining the Pokemon, which were stolen by thugs. The player tries to clear up the confusion, but the police doesn't let them go without proof. The player eventually finds the real thugs, and Team Silence is released.
Underwater Battles are restricted to Pokemon that can swim and breath underwater. These underwater battles take place underwater after the player uses Dive. These were derived for Sky Battles.
A new type has been introduced, the Pie Type. This type was added merely for fun, but were later decided to actually be developed. It is strong against Fire and Fighting types, weak against Water and Poison types, and it resists Fire, Electric and Bug types. This Pokemon also has Time Types, which originated from Pokemon Techno and Steampunk.
Players have the ability to Rollerskate, and Skateboard, both allowing the player to grind, perform tricks, and even overcome limited obstacles. Biking also returns in these games, and the Bikes are customizable. Pokemon are also rideable in this game, such as Wolflame, Tauros, Zauruscertauros, and Catrick.
This is the first game that provides voices for each and every character. Each character still has their own color for the text, but it is now accompanied with the voices.
Similar to X and Y, this game allows the player to be customized to the players liking. This feature includes hats, glasses, hair style and hair color, eye color, shirts, pants, suits, shoes, and you can adjust the height and skin color. You can also add small accessories to your Pokemon.
Pokemon Contests return from their last appearance in Pokemon Platinum. In Pokemon Centers you can make Poffins or PokeBlock which can help your Pokemon's performance in Pokemon Contests. It also introduces Group Performances and Random Performances. Group Performances are when you are teamed with another Coordinator, and must think of a Double Performance together. Random Performances are when you are given a random Pokemon for the contest. It also has Mulch, and some different colored Ball Capsules, and new Pokemon Seals, such as Flash Seals, Splash Seals, and Gust Seal.
A large amount of Berries have been introduced in this game. The berries are listen here.
- Bulb Berry (Mostly used for PokeBlock and Poffins. Also raises the effect of Flash)
- Limon Berry (Based on limes and lemons. An extremely Sour Berry. It raises the defense stat by two stages)
- Mana Berry (A pink berry which heals 40 health, but is toxic to humans)
- Growth Berry (An extremely rare berry which evolves the Pokemon)
- Choco Berry (The sweetest berry in the world which strongly raises the Pokemon Happiness)
- Vixem Berry (Strengthens Fairy-Type moves)
- Dough Berry (Strengthens Pie-Type moves)
- Rambu Berry (Based on a Rambutan. It strengthens Dual-type attacks)
- Star Berry (Raises the Beauty)
- Pitaya Berry (Based on the Pitaya. It is extremely bitter, but it raises Defense, Attack and Speed)
- Resco Berry (Based on Romanesco. Can be juiced into a Potion)
- Kohl Berry (Based on Kohlrabi. Can be juiced into a Super Potion)
- Cactun Berry (Based on Cactus. Heals any status condition, but also deals 5% damge)
- Pili Berry (An extremely healthy Berry, which are only found in Volcanos)
- Luv Berry (Cures Infatuation)
- Inho Berry (Cures a Disabled move)
- Stro Berry (Poffin and Pokeblock ingrediant)
- Mellowberry (Poffin and Pokeblock ingredient)
- Cheko Berry (An extremely dry berry, but tastes great when dipped in butter. Also used for PokeBlock)
- Lily Pod Berry (A berry grown on lily pad-like plants, which tastes sweet)
- Lemna Berry (The smallest of all berries. It heals one HP, but is usually found in pods.)
- This is the first game made by Scooter/Silence.
- This is the first game to include holographic Pokedexes, which provide holograms of the Pokemon that is being identified.
- This is the second game to include 3D gameplay.
- The game includes Berry Gardening, which was last seen in Pokemon Platinum.
- HM's other then Fly and Surf are not needed until after the main story.
- It has a sequel, Pokemon Twilight.