BW122: Ash and N: A Clash of Ideals!

Pokémon entered its third generation with the 2002 release of Pokémon Ruby and Sapphire for Game Boy Advance and continued with the Game Boy Advance remakes ofPokémon Red and Blue, Pokémon FireRed and LeafGreen, and an enhanced version of Pokémon Ruby and Sapphire titled Pokémon Emerald. The third generation introduced 135 new Pokémon (starting with Treecko and ending with Deoxys) for a total of 386 species. However, this generation also garnered some criticism for leaving out several gameplay features, including the day-and-night system introduced in the previous generation, and it was also the first installment that encouraged the player to collect merely a selected assortment of the total number of Pokémon rather than every existing species (202 out of 386 species are catchable in the Ruby and Sapphire versions).

In 2006, Japan began the fourth generation of the franchise with the release of Pokémon Diamond and Pearl for Nintendo DS. The fourth generation introduces another 107 new species of Pokémon (starting with Turtwig and ending with Arceus), bringing the total of Pokémon species to 493. The Nintendo DS "touch screen" allows new features to the game such as cooking poffins with the stylus and using the "Pokétch". New gameplay concepts include a restructured move-classification system, online multiplayer trading and battling via Nintendo Wi-Fi Connection, the return (and expansion) of the second generation's day-and-night system, the expansion of the third generation's Pokémon Contests into "Super Contests", and the new region of Sinnoh, which has an underground component for multiplayer gameplay in addition to the main overworld. Pokémon Platinum, the enhanced version of Diamond and Pearl—much like Pokémon Yellow, Crystal, and Emerald—was released September 2008 in Japan, March 2009 in North America, and was released in Australia and Europe in May 2009. Spin-off titles in the fourth generation include the Pokémon Stadium follow-up Pokémon Battle Revolution for Wii, which has Wi-Fi connectivity as well. Nintendo announced in May 2009 that enhanced remakes of Pokémon Gold and Silver, entitled Pokémon HeartGold and SoulSilver, released for the Nintendo DS system. HeartGold and SoulSilver are set in the Johto region and were released in September 2009 in Japan.

The fifth generation of Pokémon began on September 18 with the release of Pokémon Black and White in Japan for Nintendo DS. The games were originally announced by the Pokémon Company on January 29, 2010 with a tentative release later that year, before the announcement on June 27, 2010, of the games' release on September 18, 2010. This version is set in the Unova region (イッシュ地方 Isshu-chihō^?, Isshu region) and utilizes the Nintendo DS's 3-D rendering capabilities to a greater extent than Platinum,HeartGold, and SoulSilver, as shown in game footage of the player walking through the Castelia City (ヒウンシティ Hiun Shiti^?) metropolis. A total of 156 new Pokémon were introduced (starting with Victini and ending with Genesect), as well as new game mechanics such as the C Gear (Cギア C Gia^?) wireless interactivity features and the ability to upload game data to the internet and the player's computer. Pokémon Black and White was released in Europe on March 4, 2011, in North America on March 6, 2011, and in Australia on March 10, 2011. On June 23, 2012, Nintendo released Pokemon Black 2 and Pokemon White 2 in Japanese for Nintendo DS, with early October releases in North America and Europe.

On January 8, 2013, Nintendo officially announced Pokémon X and Y for the Nintendo 3DS as part of the upcoming sixth generation of games. They will be rendered in 3D and have a simultaneous worldwide release in October 2013.