In the year 2059, a massive colonization fleet, the 25th Macross Frontier, embarks on a journey to find a new home for humanity. This fleet is home to over 10 million people who live in a self-sustaining environment created by the United Nations Spacy. The Macross Frontier is currently sailing through the galaxy, near the galactic center, when a top idol singer named Sheryl Nome, known as the "Galactic Fairy", comes aboard for a concert. Sheryl is a top-ranked singer in the intergalactic charts, and her popularity is rivaled only by her talent. A normal high school girl named Ranka Lee is a huge fan of Sheryl and is on her way to the concert when she meets a high school student named Alto Saotome, who is training to become a pilot in the space fighter program. However, their encounter is interrupted by an unexpected attack by an unknown alien creature known as the Vajra, which poses a threat not only to the Macross Frontier but also to the new United Nations Spacy's advanced fighter pilots. The Vajra's attacks force the VF-25 squadron, led by Ozma Lee, to intervene and protect the civilian population. What is the Vajra's power and purpose, and what choices will humanity make in response?