In the combat providence analysis system, "COMPASS2.0," heroes gather alongside human partners in a dreamlike space. The heroes have to keep fighting to produce enough energy to keep the system running. One hero named 13 is a troublemaker who refuses to find a partner. When 13 is nearly kicked out, a new player named Jin agrees to join him. Can they bring peace to the world of #COMPASS2.0?

This is the world of the battle analysis system "Compass 2.0." It's a dreamlike space where heroes gathered from numerous other worlds live together with their human partners, the players. The energy generated by the heroes' battles is essential for the operation of #Compass, and battling is their responsibility.

Once upon a time, an unidentified enemy, the Unknown, suddenly appeared. The "Super Evolutionary Railway Development Agency," had developed the "Shinkalion," a robot that transforms into a bullet train, as a countermeasure against this threat.

"I want to be a cool person who can protect something..." Taisei Oonari, a second-year junior high school student, transfers to Shinkai Gakuen Middle School in search of clues about his older sister who disappeared two years ago.

Just then, the Unknown appears for the first time in 10 years. Taisei happens to have a high aptitude value as a Shinkalion pilot, and is forced to make a decision to fight it. What is the true nature of the Unknown and what is its purpose? What is the truth that comes to light at the end of the fight? The story of the boys' determination and growth begins now.

Segawa Yuta is a freshman of a university. He lost his parents when he was small and was raised by his sister Yuri. Yuta has been living alone since Yuri got married to a middle aged man when Yuta was a junior high student.  One day, Yuri visited Yuta's apartment and asked him to take care of her three daughters while Yuri and her husband were on a trip. He unwillingly accepted the job but the plane Yuri took went missing. In order to prevent the daughters from being adopted separately by relatives, Yuta decided to take in all three girls.  A life of a strange family in a tiny apartment begins.

After experiencing the numerous trials encountered on her journey, Reina has grown as a warrior. Determined to take part in the Queen's Blade tournament, she arrives at the capital city Gainos, where Queen Aldora awaits. There gathers a number of beautiful warriors who, like Reina, are there for the Queen's Blade.

Amongst them is Reina's sister, Claudette, determined to restore the glory of House Vance; Tomoe and Shizuka, who are both fighting for their homeland of Hinomoto; Nanael who has been ordered to participate by the Archangel; and the subordinates of the Marshland Witch.

All these beautiful fighters who gather in Gainos have been one objective, to win through the Queen's Blade, the tournament to select the strongest, most beautiful queen. Who would ascend to that glorious throne? That can only be determined via battle.

The story is set four years after the first storyline and revolves around Annelotte, the rebelling knight princess who stands up to the tyranny of the new queen.