The season begins with Bloom, Stella, Flora, Musa, and Tecna returning from their summer vacation to begin their second year at Alfea. Shortly after the beginning-of-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 in the Underrealm, where Lord Darkar lives. Three of the girls and two Specialists travel to Lord Darkar's stronghold and rescue the Pixies, then return to Alfea. During their trip to rescue the Pixies, Brandon gets dragged into a marriage with the Princess of Downland, Amentia, but gets rescued. During the season Flora developed a crush on Helia a new student at Red Fountian and Saladin's nephew, she is to scared to tell him how she feels and also has some trouble talking to him.
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 need 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 Specialists from a broken ski lift. Stella admitted that she can be insecure, makes up with Aisha and therefore she earns her charmix. Tecna reconciles with Timmy and earns her charmix. Musa earns her charmix by expressing 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 (In the Nick Version, the first transformation is Charmix due to Season 2 being converted into a One-Hour Special). 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.