"Macross Delta" is set in the year 2067, several decades after the events of previous "Macross" series. The story unfolds in the Brisingr globular cluster, a region of space inhabited by various human colonies. The series introduces the Delta Squadron, a specialized unit of the New United Nations Spacy (NUNS), which operates under the tactical music group Walküre. Walküre is a group of idol singers whose songs possess the ability to counteract the Var Syndrome, a mysterious condition that drives people into a berserk state. The Var Syndrome is linked to the Windermere Kingdom, a small but powerful nation that seeks to expand its influence across the galaxy.

The protagonist, Hayate Immelman, is a carefree and somewhat aimless young man who becomes involved with the Delta Squadron after encountering Freyja Wion, a Windermerean girl who dreams of joining Walküre. Freyja's singing abilities are discovered by Walküre, and she becomes a key member of the group. Hayate, inspired by Freyja's passion, joins the Delta Squadron as a pilot, operating the advanced VF-31 Siegfried variable fighter. Together with Mikumo Guynemer, the enigmatic lead singer of Walküre, and Mirage Farina Jenius, a skilled pilot and granddaughter of the legendary Max Jenius, they form the core of the team.

The conflict escalates as the Windermere Kingdom, led by King Heinz and his knights, including the skilled pilot Keith Aero Windermere, declares war on the NUNS. The Windermereans use the power of the Protoculture ruins and their own Fold Quartz-enhanced technology to spread the Var Syndrome, aiming to destabilize their enemies. Walküre and the Delta Squadron are tasked with countering this threat, using their music and combat skills to protect the galaxy.

Throughout the series, the characters face personal and collective challenges. Hayate struggles with his sense of purpose and his growing feelings for Freyja, while Freyja grapples with her identity and the expectations placed upon her as a Windermerean. Mikumo's mysterious origins and connection to the Protoculture add layers of intrigue, and Mirage's journey involves overcoming self-doubt and living up to her family's legacy. The series explores themes of identity, loyalty, and the power of music to unite and heal.

As the war intensifies, the Delta Squadron and Walküre engage in numerous battles against the Windermerean forces. The climax involves a decisive confrontation where the true nature of the Var Syndrome and the Protoculture's legacy are revealed. The resolution sees the characters making sacrifices and forging new paths, ultimately striving for peace and understanding in a galaxy torn by conflict. "Macross Delta" combines mecha action, musical performances, and character-driven drama, creating a narrative that is both expansive and intimate within the "Macross" universe.