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Fushigi Yuugi follows Miaka Yuuki, a typical Japanese high schooler, and her best friend Yui Hongou, as they are plunged into a world of magic and adventure. Although polar opposites when it comes to grades, Miaka and Yui are extremely close. While studying at the libaray, the two friends discover a mysterious Chinese text named "Universe of the Four Gods." The best friends find that as the book is read, the story will come true, and the two are soon dragged into the world inside the book!

They land on the outskirts of Konan, a country in the midst of war with its neighbor to the east, Kutou. Soon they are rescued from some scruffy bandits by a striking young mercenary ... only to be abandoned after he discovers they have no money to pay him. Without warning, Yui is thrown back to the real world, leaving Miaka alone in the strange country, penniless and friendless.

However, Miaka manages to find her way to the capital of Konan, while Yui reads the book and follows her friend's journey. She meets Tamahome, the mercenary who helped her earlier, and captures the attention of the Emperor. Eventually, Miaka is revealed to be the "miko," or priestess, of Konan's guardian deity, Suzaku. Confused by the turmoil of war and her sudden responsibility for an entire country, Miaka has no choice but to accept her new position. She is charged with finding her "Shiciseishi," or seven protectors, and calling upon Suzaku to help Konan win the war.

These Seishi, or warriors, are seven legendary men who are destined to guard the miko with their lives. Each is represented by a constellation, possesses a special power, and bears the mark of a Chinese character on their bodies. Gradually, Miaka finds them, one by one, learning about her adopted country, testing her endurance to its limits, and discovering a deep and special love.

However, Yui inadvertantly summons Miaka back into the real world, and unexpectedly, Yui is absorbed back into the book! Unfortunately, Yui's entrance to the world of the book begins with a tragic incident which scars and changes her. She is saved by Nakago, a mysterious man who turns out to be the general of the Kutou armies. When Miaka returns to the book's world and finally reunites with Yui, she finds that her best friend has become the miko of Kutou Country's deity, Seiryuu. They are now on opposing sides!

Both sides race to find their missing Seishi and call upon their god, amidst a storm of jealousy and misunderstandings. Soon, Miaka gathers all her Seishi and begins the summoning ceremony, but a shocking discovery causes it to fail. Miaka's only chance now is to collect the Shinzaho of Genbu and Byakko, the guardian gods of Hokkan and Sairo countries. Again, the Suzaku and Seiryuu battle to be the first to find the magical items in order to call their gods. However, through devious means, the Seiryuu manage to capture both Shinzaho and call upon their god. However, things are not as simple as they seem; in the real world, Miaka's brother, Keisuke, and his best friend, Tetsuya, are frantically researching the book's history and discover its dangerous secret and the fate of the mikos.

Once Yui calls upon her dragon god, Seiryuu, chaos ensues as the world inside the book and the real world collide! Miaka and her Seishi desperately fight a losing battle against the true enemy. Ultimately, it is the power of an unconditional friendship and an unexpected sacrifice that will change the fate of both worlds.