The games are set two years after the games Pokémon Black and White, and the Unova region has changed drastically with new locations and Pokémon from previous generations. The player - Nate, the male protagonist, or Rosa, the female protagonist - starts in a location southwest in Unova calledAspertia City with Hugh, the player's rival. They are given astarter Pokémon - Snivy, Tepig, or Oshawott - by Bianca, who is now Professor Juniper's assistant. As they venture out in Unova, they will challenge new and old Gym Leaders and encounter the new Team Plasma, while also meeting the old Team Plasma.
Near the end of the game, the Neo Team Plasma's plan is revealed. They want to freeze Unova using their technology and the power of the legendary Pokemon, Kyurem. At the Giant Chasm, Ghetsis orders Kyurem to freeze the player! Thankfully, N and his dragon (Zekrom in Black 2 and Reshiramin White 2) save the player in time. Ghetsis then uses the DNA Splicers that were stolen earlier on Kyurem, whose frozen wings shatter, revealing a set of energy asorbing node-like appendages! Kyurem then blasts N's dragon, sealing it back up in the Dark/Light Stone! Then under Ghetsis' orders, Kyurem absorbs the stone, fusing the two dragons together to make an even stronger dragon, Black/White Kyurem! The player then defeats the dragon, seperating it back into two, N's dragon is given back to him, while Kyurem flees to re-gain it's strength. After a battle with Ghetsis, he suffers a mental breakdown, and is taken away by the Shadow Traid.
Post-game, after a battle with N and his dragon, he kindly lets his dragon go, and gives the Dark/Light Stone to the player. Then the player can bring it to Dragonspiral Tower where he/she can catch N's dragon. If the player catchs N's dragon, Kyurem will re-appear at the Giant Chasm where the player can catch it too.