After being threatened by extinction at the hands of alien invaders called the Zentradi, humanity undertook the task of guaranteeing itself a future by launching fleets of colony ships into space. On Macross Frontier, one such fleet, high school student Saotome Alto's life is changed forever: the fleet is suddenly attacked by unidentified creatures while he is performing aerial stunts for a concert by the wildly popular idol Sheryl. Alto quickly finds himself in the cockpit of a new-model fighter struggling to protect Ranka Lee, a young girl he met only hours earlier, from the invaders' swath