Yuusei Fudou is out to get back what was stolen from him. The world of dueling has evolved, with Riding Duels becoming the peak of entertainment for the residents of Neo Domino City. They are played on D-Wheels, a hybrid between Duel Disks and motorbikes. After the mechanically skilled Yuusei managed to build his own D-Wheel, his former friend Jack Atlas stole it alongside Yuusei's best card, Stardust Dragon; ditching their decrepit hometown of Satellite, he escaped to Neo Domino City. In the two years since then, Jack has risen to the top of the dueling world, while Yuusei has been making preparations thanks to the help of his friends. With his new D-Wheel finished, he now sets off to Neo Domino City, his only goal to find Jack. Unbeknownst to either of them, there are far bigger things at stake than they can imagine, with puppeteers pulling the strings behind the scenes. [Written by MAL Rewrite]

After defeating a mysterious enemy, Yuuma Tsukumo, along with the help of Kaito Tenjou and Ryouga "Shark" Kamishiro, has thwarted the Barians' plans. However, Yuuma is still on a quest to retrieve the Number Cards to restore Astral's memories. The Seven Barian Emperors catch wind of Yuuma and Astral's endeavors and begin to collect the cards themselves to achieve their ultimate goal: destroying Astral's world in exchange for saving their own. Though only five of the emperors are present, they unanimously decide on annihilating Astral and Yuuma once and for all. Elsewhere, with their newfound powers of ZEXAL, Astral and Yuuma work to eliminate the enemy force that threatens Earth and the rest of the universe. Yu☆Gi☆Oh! Zexal Second unveils the mysteries and unpleasant surprises that lie in the wake of Yuuma's adversities. As Astral struggles to accept his past and the consequences it may have brought, will the gods continue to shower their fortune upon Yuuma on yet another perilous adventure?

In the bustling and futuristic city of Heartland, a young boy named Yuuma Tsukumo has a dream that everyone his age wants to achieve—earning the title of the greatest duelist! Sadly, due to his lackluster dueling skills, this dream is far from achievable. But when the school bully, Ryouga "Shark" Kamishiro, splits the key given to him by his father into two pieces, he inadvertently sets Yuuma on a collision course with his dream. Retaining one half of the key, Yuuma begins a duel with Shark, but soon realizes that his inexperienced skills are no match for him. In a sudden turn of events, Yuuma's key repairs itself, and the "Door of Destiny'' appears before him. Using the key to open it, Yuuma is greeted by an alien by the name of Astral—a being only he can see. The bewildered Yuuma soon learns that his memories have been divided into 100 "Number Cards," all of which he must retrieve. However, he is also not the only one looking for them. Bombarded by these revelations, Yuuma, alongside Astral, must defend the world from the upcoming threats that loom over Heartland City—regardless of any divine intervention that may occur.

Akazukin Chacha is the story of a young magical girl (Mahō Shōjo) named Chacha. Living with her guardian in a cottage on Mochi-mochi mountain is Seravi, who is her teacher and also the fictional world's greatest magician. Chacha is clumsy in casting her spells because, throughout the anime, when she summons something, it often turns out to be something that she didn't mean to cast, for example, spiders (kumo) instead of a cloud (also kumo). At times in the anime when she and her friends are in trouble, however, her spells do work. Living on the same mountain is a boy gifted with enormous strength named Riiya. It is described that Riiya came from a family of werewolves who can instantly change into a wolf whenever they want. Quite far from Mochi-mochi mountain lies Urizuri mountain. Dorothy, also a well known magician in her land, lives in a castle on Urizuri mountain. Living with her is Shiine, her student. Shiine is adept when it comes to casting spells. He is a young wizard and most of his knowledge about magic was taught to him by Dorothy. The first 2 seasons were originally created by the anime team. Most of the stories in season 3 are based on the manga.