In Universal Century 0079, forces of the Earth Federation and Principality of Zeon engage in a battle within the Thunderbolt Sector during the One Year War. This section of space—known for its constant strikes of electricity—proves to be a deadly battlefield, as Federation pilot Io Fleming leads a charge against Zeon's ace Daryl Lorenz and his squad of snipers. With the fighters on both sides proving to be formidable soldiers, neither side is willing to back down, fighting strategically amongst the remnants of colonies. But when Io gets a hold of a prototype Gundam, Daryl will have to make a sacrifice in order to obtain enough power to crush his enemy and ensure that Zeon is victorious, or watch as his comrades are slaughtered by a single man.

In the year 2027, the video game Phantasy Star Online 2 is all the rage at Seiga Academy. Every student is on board the fad—except for Itsuki Tachibana, a well-rounded student who doesn't play video games. Due to its popularity, the game is currently under review at Seiga Academy to see if it has a negative impact on the students. Consequently, this causes Itsuki to catch the attention of Rina Izumi, the perfectionist student council president who aims to prove that the game is not to blame. To accomplish her objective, Rina recruits Itsuki as the student council vice president and tasks him with learning to play the game while keeping his grades up. Now obliged to report his daily findings of the game to Rina and analyze its merits, Itsuki carries the fate of Phantasy Star Online 2 in his hands.

Three years ago, a bloodthirsty race of interdimensional beings known as the Disas appeared and destroyed everything they could reach on Earth. With regular weapons rendered useless, humanity's only hope of survival relied on humans who became magical girls after forming an alliance with the Spirit Realm, who had followed the Disas to Earth. After a violent conflict, the squad of magical girls emerge victorious, with the survivors now known as the Magical Five. Following the war with the Disas, the Magical Five disbands. Kurumi Mugen, Mia Cyrus, Tamara Volkova, and Lau Peipei independently continue their own military services, while their leader, Asuka Ootorii, retires and becomes a high school student. However, Asuka's peace is short-lived, as it seems there were survivors on the enemy's side as well. As magic must be fought with magic, Asuka is dragged back into combat as an even worse battle looms on the horizon.

After a brilliant victory over Saunders University High School, girls from Ooarai Girls Academy now have to face Italian-themed Anzio Girls High School in the second round of the 63rd National High School Sensha-Dou Tournament. The high-spirited girls from Anzio, led by the charismatic Chiyomi Anzai, advance toward the battle equipped with baffling tactics and a secret weapon. Ooarai will soon find out that what seemed to be a mere formality might take an unexpected and possibly disastrous turn. Whether they will win the match, or lose and doom their school to a closure, is still on a knife-edge.