The season begins with Bloom, Stella, Flora, Tecna, and Musa returning from their summer vacation to begin their second year at Alfea. Shortly after the begining-of-the-year party, a fairy girl named Aisha walks into the school and faints.
After she is brought to the school nurse, Aisha tells the Winx that several Pixies, small flying fairy-like creatures, are being held hostage by Lord Darkar. They do a test as some powers don`t work where Lord Darkar lives. Three of these girls and two Specialists travel to Lord Darkar`s stronghold and rescue the Pixies, Brandon gets dragged into a marriage with the Princess of Downland, Amentia, but gets rescued.Meanwhile, the Trix have been locked in the Fortress of Light Haven However, Lord Darkar breaks them out and gives them the Gloomix and enlists their service. Lord Darkar and the Trix begin looking for the four pieces of the Codex, the key to the realm of Realix, where the Absolute powers of darkness, the enlarged Barclays, complete the rest of the dark forces of Lord Darkar. But, as Lord Darkar discovers, he doesn't only nead the codex. He needs the shadow fire and the dragon flame, which Bloom has.
Throughout the season, the Winx and Specialists attempt to stop the Trix from stealing each piece of the Codex. Though they fail, one was in Pixie village, another was in red fountain, the third was in Cloud tower, and the final one was in Alfea, which Bloom stole while under a dark spell. Near the end of the season, Bloom is turned into Dark Bloom by a minion of Darkar who pretended to be Avalon (a professor who Ms Faragonda enlisted to work at Alfea) as the real Avalon who Darkar imprisoned escapes to Alfea and tell Ms Faragonda.
Also near the end of the season, the Charmix is introduced. The Charmix is a power-up to the Magic Winx transformation, and consists of a chest pin and shoulder/waist bag. The fairy earns her Charmix by facing her fears. Bloom earns her charmix by using her quick thinking to save the Winx and Spelialists from a broken ski lift. Stella gave up her beach fashion show to help Aisha therefore, she earns her charmix. Tecna reconciles with Timmy and earns her charmix. Musa earns her charmix by experssing her feelings to Riven, Aisha earns her charmix by facing her fears and caring for others, and Flora earns her charmix by saving the flower of Life and confessing her love to Helia. At the end of the season, the Winx and the Specialists are able to free Bloom from Darkar's control. The Winx defeat him with a final Charmix convergence and Aisha joins the Winx Club.
- The Shadow Phoenix (Back to School)
- Up To Their Old Trix (Princess of Tides)
- Rescue Mission (Into the Under Realm)
- Princess Amentia (Queen of Perfection)
- Magic Bonding (Rescuing the Pixies)
- Runaway Groom (My Boyfriend`s Wedding)
- The Mysterious Stone (The Dark Tower)
- Party Crasher (Party Monster, The Spoilsport)
- Professor Avalon`s Secrets (The Secret of Professor Avalon)
- Crypt of the Codex (The Crypt of Code)
- Race Against Time (Race Against the Time)
- Win-x Together (Together for the Victory)
- Invisable Pixies (The Lady of the Ball)
- Battle on Planet Eraklyon (Battle on Planet Eraklyon)
- The Show Must Go On (The Show Continues)
- Hallowinx (Hallowinx)
- Twinning with the Witches (Twinning with the Witches)
- In the Heart of Cloudtower (In the Heart of Cloudtower)
- Spy in the Shadow (The Spy in the Shadow)
- Pixie Village (The Village of Pixies)
- Charmix Power (The Power of Charmix)
- Danger in the Wildland (Wildland: The Great Trap)
- The Time for Truth (The Moment of Truth)
- Darkar`s Prisoner (Prisoner of Darkar)
- Face to Face with the Enemy (Face to Face with the Enemy)
- The Phoenix Revealed (The ashes of the Phoenix)