In an era when Samurai ruled Japan… The Shinsengumi has been wiped out by an unknown attacker, leaving one survivor. Seven criminals are chosen as doubles for the Shinsengumi. To protect the security of Kyoto, a top-secret replacement operation is executed.

As another year begins at Yuigaoka Girls' High School, ushering in a fresh batch of students, the school idol club Liella! is excited to expand their membership. However, Liella! is extremely popular due to the astounding talent they have continuously displayed; thus, new students lack the courage to even consider approaching the club, fearing the rigorous training that might lie ahead. Amid her worries, club leader and co-founder Kanon Shibuya meets first-year student Kinako Sakurakouji and tells her about the world of school idols. This leaves Kinako in awe, but being fairly average herself, she feels she would not be capable of matching the spirited performances of the brilliant Liella! members. Nonetheless, Kinako receives encouragement to join the group and comes to share their dream of reaching for the stars once again in the grand Love Live! Competition.

The number of terrorist acts in Japan has never been lower, thanks to the efforts of a syndicate called Direct Attack (DA). The organization raises orphaned girls as killers to carry out assassinations under their "Lycoris" program. Takina Inoue is an exceptional Lycoris with a strong sense of purpose and a penchant for perfection. Unfortunately, a hostage situation tests her patience, and the resulting act of insubordination leads to her transfer out of DA. Not thrilled about losing the only place she belonged to, she reluctantly arrives at her new base of operations—LycoReco, a cafe in disguise. Takina's new partner, however, turns out to be quite different from what she imagined. Despite being the famed Lycoris prodigy, Chisato Nishikigi appears almost unconcerned with her duties. She drags Takina along on all kinds of odd jobs under the simple explanation of helping people in need. Takina is even more puzzled when Chisato takes down a group of armed assailants without killing any of them. Feeling like a fish out of water, Takina itches to get reinstated into DA—but Chisato is determined to prove to her that there is more to a life than just taking them.

College student Yuuhi Amamiya's monotonous life is turned upside down with the appearance of Sir Noi Crezant, a talking lizard claiming to be a knight of justice. Crezant elaborates that the world is in peril—threatened by the mage Animus who wishes to annihilate it with his Biscuit Hammer, an enormous structure suspended in Earth's orbit. As the newly appointed Lizard Knight, Yuuhi must fight alongside other Beast Knights to protect the princess and save the planet from destruction. Unimpressed by the prospect of risking his life, Yuuhi continues his day as usual—until a golem created by Animus suddenly confronts him. Yuuhi is instantly overpowered, but his neighbor, Princess Samidare Asahina, luckily rescues him. To his surprise, Samidare's intention starkly differs from Crezant's; instead of saving the world, she aims to destroy it with her own hands. Captivated by her firm ambition, Yuuhi resolves to become stronger and help Samidare realize her goal. As the pair continues to fight against Animus' golems, Yuuhi finds himself gradually gaining an interest in life—but the chains of his past trauma may restrain him from progressing further.