Music idol Sheryl Nome arrives at the Macross Frontier fleet for a concert performance. In the meantime, fleet command deals with an unidentified & powerful alien enemy.

Overwhelmed by the new enemies' speed & power (despite their lesser numbers), fleet defenses cannot prevent some of the alien bio mecha from penetrating the main colony ship. Teenage music fan Ranka Lee, young student Saotome Alto & S.M.S. VF-25 veteran pilot Ozma Lee are all involved in the ordeal.

Ranka Lee is on her way to S.M.S. to drop off some items for her older brother Ozma Lee when she happens to meet Sheryl Nome. Alto Saotome also shows up when the two arrive at an observation park, but then the Vajra loom over from the skies above.

Sheryl comes across Alto again in her quest to find her missing earing. She orders Alto to guide her around the Macross Frontier fleet. Elsewhere, Ozma and Ranka argue about her decision of becoming a singer.

The members of S.M.S Macross Quarter investigate the truth behind the destruction of the 117th Large Scale Research fleet in a Vajra attack and Ozma Lee finds the shadow of Grace O' Connor's ambition present in the incident where Ranka lost her family. Meanwhile, the NUNS military forces of Frontier prepare for a final decisive battle to protect the fleet from the Vajra.