
The Winx Club begin their third and final year at Alfea. As fairies, the six best friends learn of their full-fledged fairy form, Enchantix, that can only be achieved when a fairy rescues someone from his or her own home planet and shows great courage, bravery, self-sacrifice, and compassion in doing so. Meanwhile, in the Omega Dimension, the Trix find and release a powerful and vengeful wizard named Valtor, who has a tragic connection to Bloom, as he was directly involved in the destruction of Bloom's home world, Domino, seventeen years ago alongside the three Ancient Witches. They choose to forge an alliance and plan to invade several areas in the realm of Magix and seek vengeance on those who imprisoned them by stealing their exceptionally strong, magical and mystical treasures and immeasurable power sources of each realm.

Stella's father, King Radius is throwing a princess ball for her, and he promises her a special surprise. The Trix awaken Valtor and try to escape from the Omega Dimension. Aisha must return to her realm urgently. Meanwhile, Stella and another girl, Chimera, are fighting over a dress for her princess ball.

At the party, Stella's special surprise turns out to be more of a shock, as King Radius has announced his engagement to Countess Cassandra. Chimera also casts a spell on Stella, turning her into a monster.

The Winx help Stella escape Solaria and seek help to break the spell cast upon her.

The Winx Club as well as Brandon, Timmy and Sky continue their dangerous journey to the Ice Caves to find the Mirror of Truth and turn Stella back to her usual self.
Then, the Alfea school year starts and the girls are reunited with Layla who tells them of the horrible news from Tides. Also, Ms. Farragonda tells the third years about earning their Enchantix!

Bloom, Flora, Techna, Musa, and Layla all journey to the Realm of Tides. Stella stays behind at Alfea to make sure the teachers don't find out that they left campus without permission.

The Winx Club head to the bottom of the ocean where they come across a legendary sea monster and try to gain Layla's sight back.

The gang tries to escape detention, and to get to a party on Erakylion. Meanwhile, Layla and Stella teach Bloom princess demeanor. Baltor once again is up to no good with the witches and even Princess Diaspro. Mrs. Faragonda lets us in on some secrets about Blooms mysterious past.

During a party on Sky's home planet, Princess Diaspro, aided by Valtor, launches her plan to gain the affections of Prince Sky. While doing this, she damages Bloom's feelings as he states that he is Diaspro's boyfriend. During their attempt to escape from Eraklyon, Stella earns her Enchantix after saving her dad from a dragon's attack.

The Winx and Brandon and Riven devise a plan to figure out Sky's erratic behavior and go to Eraklyon. In the end, Stella breaks the spell on Sky. The girls have to leave without knowing it worked, but Brandon is arrested.

Baltor takes over Cloud Tower and brings the witches under his control and forces them to attack Alfea after he imprisons Griffin. Fairies fight the witches while Baltor goes into battle with Farragonda!

As the Winx Club go out on a search for Faragonda they find themselves at Cloud Tower- face to face with Baltor!

The Winx Club go to Flora's home planet seeking guidance in breaking the spell cast on Ms. Faragonda. Flora's younger sister, Miele, tags along. Flora earns her Enchantix after saving her sister from the poisoned tears of the Black Willow and dumps the trix (who are sent to stop them from gathering the tears) into the Black Willow's tears where they turn into little girls.

Valtor's conquest over Aisha's home world threatens to destroy both the planet Andros and the Omega Dimension. The Winx must stop the destruction and the escaped prisoners from the Omega Dimension, and one of them will ultimately have to make a supreme sacrifice to do it. Volunteering to close the portal herself, Tecna earns her Enchantix in the process, but is seemingly lost forever in the Omega portal.

Heartbroken at the loss of Tecna, the five Winx girls go to confront Valtor at Cloudtower. Bloom learns the fate of her real parents, that they have disappeared in the fight against the Ancestral Witches and were presumably killed in the process. In the end, Sky returns with Brandon, saying Diaspro has been banished for her crime, while Bloom departs for Pyros, the Island of Dragons, to train herself to become strong enough to fight Valtor.

Bloom arrives on Pyros, an island inhabited by dragons, where she is instantly attacked and becomes stranded. She meets a dragon who is friendly and teaches her how to be a dragon. Meanwhile, back at Redfountain, Timmy dedicates all his time into finding Tecna in the Omega Dimension through his computers.

Bloom continues her exploration of Pyros and encounters a sorceress named Mya, who offers to train Bloom and help her become stronger. Meanwhile, the Winx Club and the Specialists arrive at Tecna's approximate location in the Omega Dimension. Back on Pyros, Bloom must battle the Trix by herself, but by believing in herself and refusing to give in to Valtor, she earns her fullf-ledged Enchantix and goes back to Alfea.

Sky and Bloom rescue Tecna. After falling off a ledge, Tecna and Bloom find the other Winx girls, who are trapped by ice snakes. With their help, they manage to escape with the Specialists. The Winx Club and the Specialists return to Alfea, where the girls celebrate their reunion with a party.

Valtor announces his plan to steal a relic associated with the destruction of Domino. Ophir, who is interested in Aisha (Layla) because she is his bethrothed, aids the Winx in defending the museum.

Countess Cassandra announces plans to marry Stella's father, prompting Stella and the Winx Club to crash the wedding. The boys help them ride their bikes so they can act like a bike gang, due to the tight security. In the end, Stella reverses the effects of Cassandra's magic on her father.

While the Winx Club are away on a mission, their Pixies defend their village from Icy, Stormy, and Darcy winning in the end.

The Winx proceed with a plan to negate and ultimately defeat Valtor by going to the Golden Kingdom. Ophir becomes a stowaway on their mission. They are attacked by pegagaurds and are left unconscious.

In order to obtain the Water Stars that can defeat Valtor, Stella, Musa, and Tecna must find their way through a maze with obstacles testing their commitment to possess the Stars.

Valtor challenges Faragonda, Saladin and Griffin of the three schools to a duel. The Winx determine the duel a diversion to occupy the headmasters while the real Valtor breaks into Alfea. While fighting, Valtor claims he absorbed the spirits of Bloom's parents and killing him will kill them along with him. Afterward, Aisha discovers Ophir is her fiancé Nabu, and her parents agree to call off the arranged marriage.

The Winx Club go to find the missing Cloud Tower crypts to contact the three Ancestral Witches who destroyed Domino. While there, Bloom learns from the Ancestral Witches that Valtor lied and her birth parents are alive, exiled somewhere in an unknown dimension even they don't know about. Meanwhile, Valtor endows the Trix with Disenchantix abilities, which the Winx destroy with combined Fairy Dust.

Valtor turns into a demon and releases the spell of the elements, fire, water, wind, and earth, to conquer Alfea, Red Fountain, Cloud Tower and Magix. The Winx are determined to stop him once and for all. In the end, everyone except Bloom thinks that Valtor is gone for good.

Valtor survives the attack and lures the Winx into a trap by kidnapping their boyfriends. Bloom is determined to rescue Sky and stop Valtor for good. At the end of the battle against Valtor, Headmistress Faragonda informs Bloom that her Enchantix powers are still incomplete, but she is now ready to find her birth parents at last.