The season begins with Bloom, Stella, Musa, Flora, and Tecna returning from their summer vacation to begin their second year at Alfea.
As Bloom reacquaints herself with her friends and the school, she wanders deep in the school halls and discovers a secret magical archive while in pursuit of a Fortune Fly (A flying seahorse-like Pixie Pet). The pixie watching over the archive tells Bloom that their meeting is fate and proceeds to foretell Bloom’s future.
The pixie says, in vague terms, that Bloom will meet a new friend, a new enemy, and have an adventure unlike any other before. The scene then cuts to reveal several new characters: Layla, a fairy, is working to rescue her friends: a group of pixies trapped by Lord Darkar. Despite her best efforts, she is only able to save one pixie, Piff. Layla then struggles out of the forest and makes it to the edge of Alfea, before fainting before the Winx Club girls.
After Layla begins recovering and wakes up, she explains why she was seen coming from forest and requests help to rescue the pixies, a request accepted by Ms. Faragonda, the Winx Club, and the Specialists.
Lord Darkar frees The Trix from prison in order to have them assist him in finding pieces of the Codex – a powerful source of magic guarded by the pixies. Layla joins the Winx Club, and the second attempt to rescue the remaining pixies succeeds. Throughout the rest of the season, the Winx Club work together with the pixies to help them and protect the Codex and the pixie village.