The Aether is sortied to counter another Vár Syndrome infection on a New U.N. Spacy squadron, but tensions arise when Mirage is outnumbered in a dogfight and the Aerial Knights come close to killing Walküre, and Hayate is forced to stain his hands with blood for the first time in order to protect her.

Shortly after returning to Ragna, Hayate is revealed to have fold receptors in his body, which is why he resonates flawlessly with Freyja and is immune to the Vár Syndrome. Hayate and Mirage confront Messer over his Vár Syndrome infection, before accidentally discovering a song recorded by Kaname. As the duo attempt to help him, their closeness brings a lingering feeling of anxiety to Freyja, when suddenly, the Aerial Knights launch an attack on Ragna itself.

Due to his infection, Messer is relieved from the Delta Flight and reassigned to work as an instructor, but not before showing his gratitude to Kaname. Meanwhile, the Windermereans learn how to use the power of the ruins to their favor and launch an attack on the planet Al Shahal. Walküre and Delta Flight face a tough battle there against the Aerial Knights when Messer returns to assist them. In the occasion, Keith challenges him in order to settle their rivalry once and for all.

Just as the Macross Elysion enters Al Shahal's orbit, the Sigur Berrentz folds right in front of the full N.U.N.S. defense fleet within Ragna, but not before the Macross Elysion damages its sound wave system. The Aerial Knights scramble to defend their flagship until the system is back online. Right when the Sigur Berrentz hovers near Barrett City, the N.U.N.S. detonate a reactive bomb within the Protoculture ruins. The Windermerean flagship survives the explosion, while the ruins form a larger structure that merges with the ship, effectively amplifying Heinz's song and bringing Ragna under control of the Vár Syndrome. Chaos scrambles to evacuate as many of Ragna's citizens as possible while Delta Flight engages the Aerial Knights in a dogfight and Freyja unleashes her true potential.

Aboard the Island, Makina and Chuck plan a surprise party for Freyja's 15th birthday. Hayate and Mirage go shopping for a present while Makina, Reina, and Chuck spy on them. On the night of the party, Freyja gives a speech about her childhood on Windermere and what she did to become a member of Walküre before Hayate arrives with his gift to her.

Freyja is called along Hayate for an experiment to measure the effects of her singing into his body, but concerned about his wellbeing, she finds herself unable to sing. Meanwhile on Windermere, Keith is in doubt regarding Roid's true intentions and asks his squadmates, the twins Theo and Xao Jussila, for a favor. Worried that Freyja might leave Walküre for his sake, Hayate decides to resign from the Delta Flight, but Freyja insists that she is the one who must step down, until Mirage lectures both to not relinquish their dreams and careers for each other. With Mikumo still on the medical bay and off limits to visitation, Kaname, Makina, and Reina decide to infiltrate the place in order to find her, but they are caught midway and while Makina and Reina are arrested, Kaname discovers the place where Mikumo is being held.

Following the crash of their shuttle, Mikumo, Makina, and Reina hide in the forest to evade detection by Windermerean forces. Freyja leads Hayate and Mirage to her village while Arad and Kaname enter an abandoned N.U.N.S. garrison. Mikumo is captured by Roid while Hayate, Freyja, and Mirage are cornered by the Aerial Knights, who confront Hayate over his father's sins and Freya over her betrayal before bringing them to the site of the dimensional bomb.

With the N.U.N.S. fleet wiped out by their own weapons, the final battle on Ragna is now just between Chaos and the Windermereans. Seeing the burden of shouldering the deaths of countless lives, Heinz ponders on negotiating peace talks with the N.U.N.S. while Roid prepares Mikumo on the Star Temple. Heinz orders Mikumo to sing the Song of the Stars, sending delta waves throughout the Brísingr Cluster, only to realize that Roid's objective is to bring the entire galaxy under his sole control in a Vajra-style hive mind. As both factions are mentally trapped by Mikumo's song, Heinz urges the Aerial Knights to take down Roid while Freyja tries to free her comrades from the spell. Hayate, Freyja, and Mirage's feelings for each other enable Chaos and the Aerial Knights to break free, and the combined might of Walküre releases Mikumo from Roid's control before both factions break through the Star Stage. As Hayate, Mirage, and Freyja rescue Mikumo, Keith ends the conflict by killing Roid before he himself is consumed by the destruction of the Star Stage. In the aftermath of the battle, Heinz orders the remaining Windermerean forces to retreat as the Brísingr Cluster is freed from Windermerean control.