Macross Delta is set in the year 2067, eight years after the events of Macross Frontier. The story focuses on Walküre, a team of talented idols and the Delta Squadron, a team of experienced Valkyrie pilots as they battle against the Var Syndrome, a mysterious phenomena that is consuming the galaxy, alongside the mysterious Aerial Knights Valkyrie fighter team of the Kingdom of Wind. This film recompiles scenes from the television anime with new scenes to tell a different story.

Eren Yeager and others of the 104th Training Corps have just begun to become full members of the Survey Corps. As they ready themselves to face the Titans once again, their preparations are interrupted by the invasion of Wall Rose—but all is not as it seems as more mysteries are unraveled. As the Survey Corps races to save the wall, they uncover more about the invading Titans and the dark secrets of their own members.

Several hundred years ago, humans were nearly exterminated by Titans. Titans are typically several stories tall, seem to have no intelligence, devour human beings and, worst of all, seem to do it for the pleasure rather than as a food source. A small percentage of humanity survived by walling themselves in a city protected by extremely high walls, even taller than the biggest Titans. Flash forward to the present and the city has not seen a Titan in over 100 years. Teenage boy Eren and his foster sister Mikasa witness something horrific as the city walls are destroyed by a Colossal Titan that appears out of thin air. As the smaller Titans flood the city, the two kids watch in horror as their mother is eaten alive. Eren vows that he will murder every single Titan and take revenge for all of mankind.

Several hundred years ago, humans were nearly exterminated by Titans. Titans are typically several stories tall, seem to have no intelligence, devour human beings and, worst of all, seem to do it for the pleasure rather than as a food source. A small percentage of humanity survived by walling themselves in a city protected by extremely high walls, even taller than the biggest Titans. Flash forward to the present and the city has not seen a Titan in over 100 years. Teenage boy Eren and his foster sister Mikasa witness something horrific as the city walls are destroyed by a Colossal Titan that appears out of thin air. As the smaller Titans flood the city, the two kids watch in horror as their mother is eaten alive. Eren vows that he will murder every single Titan and take revenge for all of mankind.