Several days after the mortal battle against Link Joker which embroils the whole world, the world has returned to peace. But Kai Toshiki faces a surprising situation. Sendou Aichi, the hero who saved the world from the invasion of Link Joker, has suddenly disappeared. In addition, everyone's memory about Aichi is lost...Almost all hints have been lost, and Kai starts to search Aichi with "Blaster Blade" and the deck of Royal Paladin, the only existing hint and the proof of their bonds. Kai is approached by fighters who call themselves "Quatre Knights". The four---Gaillard, Neve, Ratie and Sarah---are fighters with world-class power in vanguard fights. They control mysterious power and urge Kai to give up searching Aichi. What is their purpose...!? And what is their relationship with Aichi...!? Kai, with the new power "Legion" in his hand, fights to take Aichi back. Now, the war has begun! (Source: Cardfight!! Vanguard Wikia)

Haruto Kirishima lived a calm life out in the countryside, away from the fast-paced life of the city. Then Yuzuki Eba appeared in his life out of nowhere, having come from Tokyo to briefly live with her family. Their time together left him enamored with the memories of that short period before she just as abruptly disappeared from his life, and left him full of questions. Kimi no Iru Machi begins some time later, after Haruto moves to Tokyo to live with his sister, in order to pursue a career as a cook. In reality though he wishes to be with Yuzuki. Things don't start good though. When he arrives he is mistaken for a burglar and attacked by his sister's neighbour Mishima Asuka. After the misunderstanding is cleared his feelings begin to waver though. Is Eba, who keeps avoiding him for seemingly no reason, the one for him or is it Asuka?

The continuation of Yurumates 3D right after the first season.

Yurume, an 18-year-old "ronin" and recent high school graduate, has high hopes of being accepted and attending Tokyo University. She moves into an apartment complex, the Maison du Wish, located on the outskirts of Tokyo where other ronins living there are studying for upcoming college acceptance exams.