The film revolves around a mysterious girl named Éclair who appears before Fairy Tail, the world's most notorious wizard's guild. She lost all of her memories, except for the imperative that she must deliver two Phoenix Stones somewhere. The stones may spell the collapse of the magical world, and Natsu, Lucy, and the rest of the Fairy Tail guild are caught up in the intrigue.

A superficial but kind-hearted celestial mage, Lucy Heartfilia, joins a famous wizarding guild in Magnolia Town called Fairy Tail, where the members use their powers to earn rewards in exchange for fulfilling quests. Here she befriends an impetuous but faithful dragon-slayer wizard, Natsu Dragneel, who is scouring the land for his missing father. The two form a bond with fellow mages Erza Scarlet and Gray Fullbuster, and together they tackle daunting challenges, taking on several powerful allies and foes along the way. Created by Hiro Mashima, Fairy Tail is an action-packed adventure that follows Lucy and her friends as they learn the value of friendship, forgiveness and family.

Continuing from where Season 1 left, the story continues with a more in depth into the characters but with the same humor narrative as before.

The story centers around Akihisa Yoshii, the "baka" of the title. His academy rigidly divides up the student body into classes based on the results of tests. The prodigies are in the A class with reclining seats complete with air conditioning, but Akihisa is in F class, the lowest rung of the school ladder which is furnished only with low, decrepit tables and worn-out straw tatami mats. A girl named Mizuki Himeji is actually one of the smartest girls in Akihisa's sophomore year, but she had a fever on test day and was pigeonholed into the F class. Besides Mizuki (who Akihisa secretly adores), the F class also has Yuuji Sakamoto, the class president who has been Akihisa's friend and partner-in-crime since the freshman year. The school happens to have developed experiments to summon fantasy creatures, and Akihisa decides to rally F class to take on the higher-tiered classes and seize their perks. The F class uses the summoned creatures in an all-out battle for school supremacy.