Less than a year after the events that transpired in the Macross 7 TV series, Basara leaves Fire Bomber and travels to the planet Zola. There, he meets a girl named Elma, who is a big fan of Fire Bomber. It is also on this planet where he must once again use his Spiritia powers; this time, to stop an army of poachers and Elma's father Graham from killing a group of space whales travelling within the planetary system.

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.

In the small, impoverished Tison Village of the Parthevia Empire, a boy, Sinbad, is born to the jaded ex-soldier Badr and his kind-hearted wife Esra. His birth creates a radiant surge throughout the rukh, a declaration of a singularity to those who stand at the pinnacle of magical might: the Child of Destiny is here. Despite his country being plagued by economic instability and the repercussions of war, Sinbad leads a cheerful life—until a stranger's arrival shatters his peaceful world, and tragedy soon befalls him. Years later, mysterious edifices called dungeons have been erected all over the world. Rumored to contain great power and treasures, these dungeons piqued the interest of adventurers and armies alike; though to this day, none have returned therefrom. Sinbad, now 14, has grown into a charming and talented young boy. Inspired by the shocking events of his childhood and by his father's words, he yearns to begin exploring the world beyond his village. As though orchestrated by fate, Sinbad meets an enigmatic traveler named Yunan. Stirred by Sinbad's story and ambitions, Yunan directs him to a dungeon which he claims holds the power Sinbad needs to achieve his goals—the power of a king. Magi: Sinbad no Bouken tells the epic saga of Sinbad's early life as he travels the world, honing his skill and influence, while gathering allies and power to become the High King of the Seven Seas.

A Magi is a magician whose inclination toward magic is so immense that they can be said to shape the world. With their significant influence, each Magi chooses a worthy candidate to become a king, then helps them conquer strange labyrinths called Dungeons and acquire the power of mythical djinns within. Above all else, the Magi supervises their elected representative as they build a country that might one day bring the world to its knees. Aladdin is a young Magi wandering the world in search of his true self. However, his journey is not a lonely one, as he is accompanied by his friend and mentor Ugo—a djinn he summons using his flute. In his travels, Aladdin also befriends Alibaba Saluja and guides him to a nearby Dungeon. With this newfound friendship, they begin an epic adventure across the world, witnessing various irregularities that seem more frequent than ever.