In 2059, five decades after the Space War I conflict seen in the first Macross story. Macross Frontier, the 25th New Macross Class super-long-distance colonization fleet, is journeying through the galaxy to a new paradise to call home. However, it is locked in a state of war with a strange enemy called Vajra. Macross FB7 is the 30th anniversary work of the Macross franchise.

In a city filled with anthropomorphic cat-people, Catman lives free of rules and boundaries, doing everything he wants, which often collides with the other iinhabitants of the city. Created entirely in flash, with no spoken dialog, Catman instead speaks in English and Japanese subtitles. The series is spread across three so-called 'seasons', with only the third having been aired.

A side story taking place somewhere before the second half of the series, prior to Daba acquiring the L-Gaim Mk-II. Daba's comrade Leccee is captured by Poseidal's forces, and Daba and his rebels attempt to save her.

Having failed the Comet Blaster exams mysteriously, Mikaze and her friends are sent back to the Shimoji Island base, where, with three new Meteor Sweeper trainees around, they have been promoted to instructor positions. Meanwhile, more comets are on their way to Earth, and the mysteries behind the rift in the Cosmic Emergency Management Agency—as well as the alien parasites—begins to unravel.