Zekrom and Reshiram were originally part of the same Dragon that helped create the Unova Region with the assistance of two brothers. The two brothers began to bicker over who was right. The Dragon split itself into two Dragons who then sided with either brother.
Eventually, the Dragons became tired from the constant fighting. They created the Unova Region and transformed into the Dark and Light Stones to try and restore their former strength. The Legend eventually passed into obscurity, with Zekrom and Reshiram awaiting a hero to awaken them.
Pokemon Black and White
During the course of Pokemon Black and White versions, Team Plasma's King - N - finds Zekrom/Reshiram (respectively) at the top of Dragonspiral Mountain. The Dragon leaves, forcing the player to discover the location of the Light/Dark Stone needed to awaken the other dragon.
After first investigating the Ruins beneath the Desert Resort, the player is called by Professor Juniper to Nacrene City, where they believe they have found the Dark/Light Stone. This is hinted earlier in the game when the player first arrives at the Museum and discovers the "boring old rock" on the pedestal.
Eventually, the player brings the respective Stone to N's Castle, and must capture the Dragon in order to proceed with the rest of the story. However, should they defeat the Dragon instead, it will reappear at the top of Dragonspiral Tower
Pokemon Black 2 and White 2
In Pokémon Black 2 and White 2 after many hardships, the player confronts New Team Plasma's leader, Ghetsis, along with Kyurem at Giant Chasm. N and Zekrom/Reshiram also arrive to stop Ghetsis' plans. Ghetsis activates the DNA Splicers item, which causes Kyurem to force Zekrom/Reshiram to assume their forms as the Dark/Light Stone. It then absorbs the stone and transforms into Black/White Kyurem for the player to battle. After this, Kyurem releases the Dragon and vanishes.
Later on, the player can challenge N, alongside the Dragon that matches the color of their game's version. N will revert the Dragon to stone form, if he loses, and tells the player to awaken Zekrom/Reshiram at the top of Dragonspiral Tower. After this the Light/Dark Stones do not appear.
- In the coding for Black/White, there is an item called the God Stone. This item isn't accessible in gameplay but may have been intended as Kyurem's Stone. Alternatively it may just be a dummy item used for testing purposes, as its description was "A rare stone.".