Dopo la sconfitta delle Trix e dell'Armata Oscura, le Winx iniziano il secondo anno di studi alla scuola di Alfea. Insieme alle altre studentesse si preparano per la festa di inaugurazione e ristrutturazione di Alfea, alla quale parteciperanno anche gli Specialisti. Mentre Stella cerca quale vestito mettere per l'occasione, Musa si occupa del concerto dell'evento, Tecna della posizione dei posti degli invitati e Flora dell'allestimento floreale, Bloom trova una stanza segreta ad Alfea, l'Archivio Magico, in cui vive una Pixie di nome Concorda. Nel frattempo in un castello sotterraneo, una misteriosa ragazza cerca di liberare sette Pixie dalla prigionia della Fenice d'Ombra, Lord Darkar, ma la ragazza fallisce e la Fenice, con i suoi poteri, la fa precipitare nel vuoto. La giovane si salva, ma giunge ad Alfea stremata e sviene sotto gli occhi delle Winx.

Layla is out cold in the bedroom of the Winx Club and Lord Darkar goes to the Light Haven -- the Do-Gooder's boot camp where Icy, Stormy, and Darcy are being held. He breaks them out to become his evil army. He also gives them a major upgrade on their powers.

Stella and Brandon fall into an underground river at the bottom of the chasam which sucks them down the current into a whirlpool and onto the shores near an underground kingdom called Downland where they are found by a palace guard and a centry named Sponsus who takes the couple to Amentia the perfectionist and queen of Downland. Amentia sees Brandon and takes him for her husband! A devestated and weakened Stella must soon find the sun to renew her winx or her friends will become monster chow!

Layla, Bloom, Stella, and Sky successfully reach ShadowHuant. Meanwhile, Layla saves the remaining pixies and later a mysterious man appears and rescues the four of them from the witches.

After saving the pixies, Bloom, Stella, Layla and Sky go to Downland to stop Queen Amentia from marrying Brandon.

A mysterious large dark towers appear near Alfea. As the Winx Club attempts to destroy it, their powers are drained!

The new campus for Red Fountain opens. The Winx Club joins in the grand opening celebration and meet Helia, who likes drawing. But Lord Darkar attacks Red Fountain with a monster, hoping to distract Red Fountain from Icy, Darcy and Stormy, who are trying to steal the codex.

After careful observation of Professor Avalon, Techna and Digit become convinced that he isn't who he says he is. They begin researching his past and fear he is the Angel of Doom in disguise.

Red Fountain is attacked by a chaos globe! While the Heroes are busy protecting their campus, the Witches break in and try to steal the codex. Bloom, Flora and Techna try to help the specialists gaurd the codex.

Lord Darkar hits the pixies with a spell while they're playing which makes them want to go home. The Winx Club must save the pixies and battle the monsters Darkar sends to stop them!

A boy named "Jared" has a crush on Musa, and wants to go out on a date with her. Later, Darcy casts a spell on Jared to jinx the magical chamber, and the Winx Club must combine their powers to beat the monster.

When Bloom decides to go back to Earth, Layla, Musa, and Stella decide to join her. When some gangsters catch Musa using magic, it's up to the Pixies to save them!

Sky, Bloom, Brandon, Flora, Lockette, and Zing attempt save Princess Diaspro from a a band of goodie goodies known as the Wrong Righters who attempt teach Diaspro a lesson in kindness and helping others.

Musa faces her greatest challenge ever when she must face a huge audience including her father but evil crashes the party and Stormy threatens to destroy Musa's father! Music power is put to the ultimate test to save the concert and Musa's beloved father.

The girls are invited to an Halloween party on Earth by Bloom's old rival Mitzy. The party is held in a mansion that is said to be haunted by the ghosts of three witches looking for their long lost sister.

Bloom and the rest of the Winx go to Cloud Tower to learn more about Dark Magic from the witches. Mirta and Zing go along to help out. While the girls are there, Cloud Tower is attacked by Icy, Darcy, and Stormy, who try to steal another piece of the codex!

Griffin takes back control of the Heart of Cloud Tower, providing temporary relief and a glimmer of hope. But Senior Witches soon locate the part of the codex. The Winx overwhelmed by the power of the their enemies fall back on their one last chance, convergence.

Bloom is angry for loosing two pieces of the Codex to the witches and turns to Avalon for advice. While undergoing regression therapy with professor Avalon a mysterious dark energy takes hold of Bloom. While her friends worry about her well being, Bloom ultimately makes her way to the secret room to steal Alfea's part of the Codex.

While The Winx leave for a getway resort, Avalon shows his true loyalties and tricks a pixie into going back to Pixie village. Icy follows to retrieve the codex.

Icy, Darcy and Stormy turn the creatures of the Resort Realm against the winx club girls.

Seemingly trapped by the Witches, the Winx girls and the heroes have to work together in the fight for their lives! With Timmy as head strategist, they set a trap for the Witches.

Flora, Helia, Sky, Brandon, and Layla go to the pixie village for essence from the flower of life to cure the sneezing pixies but find out it was destroyed in the battle between Icy and Livy for the codex. Ninfea encourages Flora to heal the flower of life. Meanwhile back at Alfea the Bloom, Stella, Musa, Techna and Layla Charmix train to fight Darkar. Then Musa Stella and Techna find the real Professor Avalon revealing the other to be a fake right before he kidnaps Bloom!

Bloom is in Darkar's captivity so he can unite Dragon Fire with Shadow Fire and open the portal to Realix. The Winx Club and Heroes must head for Shadowhaunt and rescue Bloom! Fortunately Amentia and the guards will help them as well, but it's too late-Darkar has turned Bloom into evil!

The magical universe enters its darkest hour as Bloom (who has turned evil) and Darkar(who has dumped the witches) combine powers to enter Realix. The Winx Club and warriors enter Shadowhaunt where they face Kerbog who has been yet again transformed into an extinct magical creature called an Octaceraton! The five fairies powers have no effect on it and when the Teachers show up to help. Is there any hope of saving Bloom?

The teachers (Faragonda, Griffon, and Codatorta) and the Pixie Elders (Athena, Discorda, Ninfea, and Concorda) help the Winx Club. With Stella's help, they are able to open another portal into Realix and the Winx Club go to save Bloom. Meanwhile, upset that Darkar dumped them, Icy, Darcy and Stormy use their powers to combine and turn into MegaTrix and they take on Darkar. The Winx Club tries to battle Darkar to release her from his spell, but are unsuccessful. While Darkar is busy battling the MegaTrix, the Heroes show up and Sky tries to talk to Bloom. Will love save her and the entire realm from Darkar?