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Pokémon Indigo Version is a game for the Nintendo DS and Nintendo 3DS, as part of Generation V. The game is a sequel to Pokémon Red, Blue, Yellow, FireRed, LeafGreen, Gold, Silver, HeartGold and SoulSilver, and takes place at approximately the same time as Pokémon Black 2 and White 2.
Mewtwo, in its Indomitable Forme, is the version mascot of the game.
The games take place two years after Gold and Silver. Giovanni, boss of Team Neo-Rocket, has risen once again, plotting to harness the power of the legendary Mewtwo to build a machine that lets him control the minds of Pokémon. Meanwhile, Pallet Town's resident Pokémon Professor, Samuel Oak, has gone missing. A young Trainer from Monkrome Town is charged by the local Pokémon Professor Quercia to investigate Oak's mysterious disappearance, and the journey begins...
- Purple: The male player character, he lives in Monkrome Town. Like the Unova protagonists, he appears to be in his mid-teenage years. He slightly resembles Red.
- Lavender: The female player character, she lives in Monkrome Town. Like the Unova protagonists, she appears to be in her mid-teenage years. She slightly resembles leaf.
- Bruce: The rival, he lives in Monkrome Town. He has a profound hatred for the player character, which is revealed to be due to deep, dark secrets and suspicions related to Oak's disappearance.
- Professor Quercia: The resident Pokémon Professor of Monkrome Town, he studies how Pokémon can help humans in everyday life. He sends the player character on a journey to find the missing Professor Oak, but has more than a few secrets up his sleeve...
- Professor Samuel Oak: The resident Pokémon Professor of Pallet Town. He has gone missing for unexplained reasons.
- Blue Oak: Professor Oak's grandson and the Gym Leader of Viridian City. He appears several times along the way to help the protagonist and Bruce.
- The game uses animated sprites for trainers and Pokémon, similar to other Generation V games.
- Although the game is set in Kanto, new areas have been added, similar to Black 2 and White 2. Bulbasaur, Charmander and Squirtle remain the starter Pokémon, however.
- The Kanto Dex has been expanded to include evolutions and pre-evolutions of Kanto Pokémon, such as Pichu, Scizor and Rhyperior.
- Mewtwo has a new Forme, Indomitable Forme. It wears the armor that it was seen wearing in the anime movie Mewtwo Strikes Back, and is said to have greater controls over its powers in this forme. Both its Attack and Special Attack are higher, but it is also much slower.
- Mewtwo is encountered in its Indomitable Forme during the storyline, under Giovanni's control. However, it must be defeated; it cannot be captured until the post-game. The player can travel to Cerulean Cave to encounter it in its regular Forme, then must go through a sidequest to obtain the equippable Power Armor item that allows it to switch formes.
- The landscape has changed since Gold and Silver, and new Gym Leaders are featured. For example, Blaine has retired, leaving his son Ivar to take up his mantle.
- Johto is available to explore in the post-game. Like Kanto, it has gone through several changes in terms of landscape, areas and characters.
- The player can use the Poké Link, which is similar to the C-Gear from Unova games.
- Like in Generations II and IV, Red is battleable again at Mt. Silver, except now in a double battle with Leaf. Leaf's Jigglypuff, like Red's Pikachu, is at Level 90 - the highest level of any Pokémon encountered in any game.
- Ethan and Lyra appear as non-playable, battleable trainers in Johto who meet the player several times.
- A special sidequest can be unlocked by connecting with Black or White similar to the Memory Link from Black 2 and White 2. The player will meet Hilbert or Hilda (depending on the chosen character from the connected game), who will have a Level 80 Reshiram or Zekrom (depending on the connected game). They will travel together in search of N, while taking on some Neo-Team Plasma grunts hiding in Kanto who were planning to undermine Giovanni. At the end of the sidequest, the B/W protagonist gives the Indigo protagonist their dragon as a special gift.
- Connecting to Black 2 or White 2 causes Kyurem to appear. If the player has cleared the Black/White sidequest, Kyurem will fuse with the Unova protagonist's dragon, and can be captured as Black/White Kyurem.
- Ho-Oh, Lugia, Rayquaza and Giratina are obtainable in the postgame.
- Bowser, from the Mario series, makes a humorous "easter egg" cameo in the Fuchsia City, where several bystanders mistake him for a Pokémon.