The world of Earth-land is home to numerous guilds where skilled wizards apply their magical abilities for paid job requests. Natsu Dragneel, a dragon slayer wizard from the Fairy Tail guild, explores the Kingdom of Fiore in search of his missing adoptive father, the dragon Igneel. During his journey, he befriends a young celestial wizard named Lucy Heartfilia and invites her to join Fairy Tail. Lucy forms a team with Natsu and his cat-like Exceedpartner, Happy, which is joined by other guild members: Gray Fullbuster, an ice wizard; Erza Scarlet, a magical knight; and Wendy Marvell and Carla, another dragon slayer and Exceed duo. The team embark on numerous missions together, which include subduing criminals, illegal dark guilds, and ancient Etherious demons created by the immortal dark wizard Zeref.
After several adventures, Natsu and his companions encounter Zeref living in isolation on the guild's sacred ground of Sirius Island. A battle over Zeref ensues between Fairy Tail and the dark guild Grimoire Heart, which attracts the attention of the evil black dragon Acnologia. The Fairy Tail wizards survive Acnologia's assault when the spirit of their guild's founder and Zeref's estranged lover, Mavis Vermillion, casts the defensive Fairy Sphere spell that places them into seven years of suspended animation. After later participating in the Grand Magic Games tournament, Fairy Tail wages war against Tartaros, a dark guild of Etherious that aim to unseal a book believed to contain E.N.D., Zeref's ultimate demon. Acnologia returns to annihilate both guilds, prompting Igneel – revealed to have sealed himself within Natsu – to emerge and battle Acnologia. However, Acnologia kills Igneel in front of a helpless Natsu, who departs on a training journey to avenge Igneel.
One year later, Natsu returns to discover that Fairy Tail's master, Makarov Dreyar, has been futilely trying to postpone an invasion by the Alvarez Empire, which Zeref governs. Zeref and his forces assault Fiore, intending to acquire Mavis' body preserved beneath Fairy Tail's guildhall, which houses a wellspring of infinite magic power called Fairy Heart. While battling Zeref, Natsu is informed of his own identity as both Zeref's younger brother and the true incarnation of E.N.D., whom Zeref resurrected as a demon with the intention of being killed by him. When Natsu fails to do so, Zeref extracts and absorbs Fairy Heart in a bid to rewrite the present timeline with one where he might prevent the atrocities he and Acnologia have caused. Natsu incapacitates Zeref to stop the drastic changes to history this would create, while Lucy edits the book of E.N.D. to make Natsu human. Mavis then lifts her and Zeref's shared curse of immortality by reciprocating his love, which kills them both.
Meanwhile, Fairy Tail and their allies detain Acnologia within a space-time rift discovered by Lucy's ancestor, Anna Heartfilia. However, Acnologia escapes while his disembodied spirit traps all of the present dragon slayers within the rift to maintain his godlike power. Lucy and the other wizards immobilize the dragon's body within Fairy Sphere, while Natsu accumulates the other dragon slayers' magic and destroys Acnologia's spirit, killing him and freeing the dragon slayers from captivity. In the following year, Lucy publishes a novel based on her experiences at the guild; at the award ceremony, two strangers resembling Mavis and Zeref meet and befriend each other. Afterwards, Natsu and his team depart on a century-old guild mission, continuing their adventures together.