"Vividred Operation" is set in a near-future world where humanity has achieved sustainable energy through the Manifestation Engine, a revolutionary technology developed by Kenjirō Isshiki. The story unfolds on an artificial island called Ōshima, where the protagonist, Akane Isshiki, lives with her younger sister, Aoi, and their grandfather, Kenjirō. Akane is an ordinary high school student who enjoys a peaceful life until the appearance of mysterious entities known as the Alone threatens the world. These alien-like beings seek to disrupt the Manifestation Engine and plunge humanity into chaos.

To combat the Alone, Kenjirō develops a combat system called the Vivid System, which requires a compatible user to wield its power. Akane is revealed to be the only person capable of synchronizing with the system, transforming her into Vividred, a powerful warrior equipped with advanced technology and weaponry. As Vividred, Akane fights to protect her home and loved ones from the Alone, which grow increasingly dangerous with each encounter.

Throughout the series, Akane is joined by allies who also gain the ability to synchronize with the Vivid System. These include Rei Kuroki, a reserved and skilled fighter; Wakaba Saegusa, a cheerful and energetic friend of Akane; and Himawari Shinomiya, a mysterious girl with a connection to the Alone. Together, they form a team to defend Ōshima and uncover the truth behind the Alone's origins. The narrative explores themes of friendship, teamwork, and the ethical implications of advanced technology, as the characters confront both external threats and personal challenges.

The plot intensifies as the Alone's attacks become more coordinated, revealing a deeper conspiracy tied to the Manifestation Engine and the true nature of the Vivid System. The series balances action-packed battles with moments of character development, highlighting the bonds between Akane and her friends as they face increasingly dire situations. The story culminates in a climactic confrontation that tests their resolve and forces them to make difficult choices to protect their world.