Team Plasma wants to set Pokemon free. Yep, you heard right. They dislike the way Pokemon are being treated, abused by many, forced to battle and so N wants to separate humans and Pokemon making the world black and white. To accomplish that, he needs the Black/White Stone to revive Reshiram/Zekrom which will help him. N manages to awake Zekrom/Reshiram and actually befriend the dragon putting it under his command.
At the end, it turns out Geechisu is N's father and how he has been manipulating his son to get what he wants. He reveals how he wanted to use the powers of Reshiram/Zekrom to become the only person who owns a Pokemon, unlike N, who only wanted their well-being. N is deeply disappointed and apologizes to the protagonist (at the very end of the game). He also releases his Zekrom/Reshiram and leaves.
At the end, it turns out Geechisu is N's father and how he has been manipulating his son to get what he wants. He reveals how he wanted to use the powers of Reshiram/Zekrom to become the only person who owns a Pokemon, unlike N, who only wanted their well-being. N is deeply disappointed and apologizes to the protagonist (at the very end of the game). He also releases his Zekrom/Reshiram and leaves.