The Trix have taken Bloom's Dragon Flame and will stop at nothing to take over all of Magix. The evil witches being their quest by taking over their own school, Cloudtower. They then build an army of villains to help them take over Redfountain, the school of the Specialists. It's battle on as those not aligned with the Trix retreat to Alfea and join forces to save the Magix realm. As the conflict rages on, Bloom finds herself drawn to the spirit of Daphne, who reveals a secret Bloom never imagined.
The Shadow Phoenix is trying to take over the Magic Dimension. He kidnaps Bloom and casts a spell on her to make her become evil so that he could use her powers to help him with his conquest.
Bloom discovers she is a fairy. She gets the chance to attend Alfea College with her new BFFs: Stella, Flora, Tecna, and Musa.