After a brutal conflict with giant beings called Zentradi, humanity seeks refuge on the Macross Frontier fleet. Amidst peace, in 2059, the aspiring mecha pilot Alto Saotome readies for a performance alongside the renowned singer Sheryl Nome. But chaos erupts when alien creatures, the Vajra, intrude during the show, endangering the city. Amidst the turmoil, Ranka Lee, a girl left behind, faces the Vajra until Alto swoops in to rescue her. Impressed by his combat prowess, the Strategic Military Services enlist Alto to combat this new alien menace.