Following a brutal war with the Zentradi, humanity has been forced to seek refuge in the core of the galaxy aboard the Macross Frontier, an armada of colonial vessels. As time passes, the threat of extraterrestrial peril fades into a distant memory and life resumes its normal rhythm. Nevertheless, during a performance by renowned singer Sheryl Nome, Macross Frontier is suddenly besieged by an attack from the Vajra, a biomechanical species of aliens, throwing the entire fleet into turmoil. Amidst the chaos, Ranka Lee becomes stranded and targeted by the Vajra, but is saved by the courageous young pilot, Alto Saotome. Recognizing his formidable combat skills, the Strategic Military Services program enlists Alto's aid in combatting this novel alien threat.