Following a catastrophic war against a race of giants known as the Zentradi, humanity has escaped towards the center of the galaxy aboard a fleet of colonial vessels called the Macross Frontier. As the extraterrestrial threat is left further and further behind, life on Macross Frontier proceeds as usual. In the year 2059, a young mecha pilot trainee named Alto Saotome and his colleagues are preparing to perform an accompanying routine for the famous singer Sheryl Nome, who has come to Macross Frontier for a concert. During the performance, a biomechanical alien species known as the Vajra make a sudden appearance, breaking through the defensive perimeter surrounding the vessel and crash-landing near the concert venue, plunging the entire city into chaos. As the concertgoers evacuate, a young girl named Ranka Lee is left behind and gets targeted by the Vajra, but she is saved at the last minute by Alto. Following these events, the Strategic Military Services program notes Alto's skill in battle, resulting in his recruitment to combat the new alien threat.

Years after his father is defeated by an adolescent Gokuu Son, Magenta seeks revenge against Gokuu's family and allies. In his quest to resurrect the defunct Red Ribbon Army, Magenta drafts the services of Dr. Hedo, grandson of the evil legendary scientist Dr. Gero. Hedo embarks to invent a new line of superheroic androids to eliminate Gokuu after Magenta manipulates him into believing that Earth's most powerful heroes are actually alien villains. While Gokuu and Vegeta train offworld, the alien Piccolo mentors Pan, Gokuu's toddler granddaughter, in the same way he once trained Gohan Son, her father. Gohan himself has forsaken his warrior lineage in order to pursue an academic career. Both Piccolo and Gohan must leap into action when their quiet lives are interrupted by the arrival of Gamma 1-gou and Gamma 2-gou—Hedo's new android creations. While the Gamma androids believe they are fighting for justice, a more sinister project incubates beneath the Red Ribbon headquarters. Gohan and Piccolo take drastic actions to protect Pan and defend the planet against a new robotic menace.

Hitomi Kanzaki is just an ordinary 15-year-old schoolgirl with an interest in tarot cards and fortune telling, but one night, a boy named Van Fanel suddenly appears from the sky along with a vicious dragon. Thanks to a premonition from Hitomi, Van successfully kills the dragon, but a pillar of light appears and envelopes them both. As a result, Hitomi finds herself transported to the world of Gaea, a mysterious land where the Earth hangs in the sky. In this new land, Hitomi soon discovers that Van is a prince of the Kingdom of Fanelia, which soon falls under attack by the evil empire of Zaibach. In an attempt to fight them off, Van boards his family's ancient guymelef Escaflowne—a mechanized battle suit—but fails to defeat them, and Fanelia ends up destroyed. Now on the run, Hitomi and Van encounter a handsome Asturian knight named Allen Schezar, whom Hitomi is shocked to find looks exactly like her crush from Earth. With some new allies on their side, Van and Hitomi fight back against the forces of Zaibach as the empire strives to revive an ancient power.

Legend tells that when the Earth was destroyed, the great clockmaker Y made a replacement from cogs and gears. Naoto Miura is a young boy who aspires to be a great clockmaker. However, despite his unique talent—sensitive hearing that can immediately understand clockwork mechanics from noise alone—he has made little progress. But this changes when a coffin falls from the sky into his apartment, revealing RyuZU, a female automaton forged by Y himself. News of RyuZU's arrival brings Marie Bell Breguet, the gifted heir of a distinguished line of clockmakers, and her cyborg bodyguard Vainney Halter into Naoto's life as well. When she and Naoto both become embroiled in an action-packed battle for their lives, they discover an uncomfortable truth: the clockwork planet that humanity has lived on for over a millennium is beginning to break down—a secret that many people will kill to protect.