Al Shahal has fallen to the Windermere Kingdom and all remaining forces still loyal to the New United Government gather on Ragna, which is their final line of defense. Knowing that the Windermereans' plan can only work with all Protoculture ruins operational, the Government makes preparations to destroy the ruins on Ragna, despite the possible consequences to the planet's environment. As the population evacuates, the members of Chaos convince the military to delay their plan to blow up the ruins as they take off with their fortress, the Macross Elysion, to commence Operation Einherjar (オペレーション・エインヘリャル Operēshon Einheryaru) confront the enemy forces.

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.