500,000 years later in the year 2025, the Megaroad-13 colonization fleet discovered an inhabitable planet and named its star system Varauta . Later in 2043 an U.N. Spacy research fleet launched an expedition to the icy fourth planet in the system and discovered a mysterious energy field and alien ruins beneath the surface. Entering a cave, the expedition encountered the source: the crystal prisons of the Protodeviln, brought back to consciousness by the arrival of fresh spiritia. High-ranking Protodeviln awakened and remotely possessed two of the expedition officers while brainwashing the rest into a new Supervision Army called the Varauta Army . After capturing the Megaroad-13 (and modifying their ships and mecha to better serve their purposes) the next target of the Protodeviln and their new Varauta army became the approaching colonization fleets, Macross 5 and Macross 7.
The Varauta initial attacks on the Macross 5 and 7 fleets escalated into a new armed conflict known as the Protodeviln War, which caused heavy casualties on both the Varauta and the U.N. Spacy sides. These included part of the Varauta Army, some of the Protodeviln, the whole Macross 5 defense fleet and part of the Macross 7 defense fleet. Survivors from Macross 5 were imprisoned and used as living batteries. After nearly an entire year of battles the war between the Macross 7 fleet and the Varauta army finally concludes thanks to the efforts of musician Basara Nekki and his band Fire Bomber, who were discovered to be the new Anima Spiritia and the only force capable of effectively stopping the Protodeviln attacks.
In the end the Protodeviln evolve into a Spiritia self-regenerating race with Basara Nekki's singing as the catalyst. Eventually the surviving Protodeviln leave to travel across the universe, now fully capable of producing Spiritia by themselves and with no need to absorb it from Humans or Zentradi anymore.