The year is 2059, nearly 47 years since humanity and the Zentradi laid down their arms and began to explore the galaxy both races called home. Realize that Earth would not forever be their home, both began the search for suitable worlds to inhabit, sending out colonization fleets modeled after the first Macross-class ship.
One particular colony, Macross Frontier, is the 55th such fleet and the 25th of the New Macross-class to embark on it's journey, headed towards the core of the Milky Way. Protected by a detachment of the New UN Spacey and a Private Military Provider, the S.M.S. or Strategic Military Services, the colony's mission is to find a world on which to settle.
After a reconnaissance mission is attacked by a powerful insectoid, biomechanical alien life-form called the Vajra, the fleet finds itself under constant threat of attack, stretching both the military and S.M.S. to protect the colony at all costs.