After barely surviving the Supsace Invasion of Tabuu in the Nintendo Universe, Spyro, Sparx, their group of lougers and Sonic end up in a city called Gardenia, where they meet Bloom, a supposedly ordinary teenage girl living a perfectly normal life on planet Earth with her mother, father and her pet rabbit, Kiko. But when Bloom and her new oddly misfit bunch of friends encounter a girl defending herself and a yellow two-tailed fox from a yellow ogre named Knut. This girl's name is Stella, a fairy princess of the planet Solaria and the yellow two-tailed fox is Sonic's genius best pal/bro, Tails "Miles" Prower. But when Bloom reveals she has magical powers after uncontrollably unleashed a blast of light during the conflect with the ogre, Stella takes Bloom, Sonic, Tails and the louge to Magix, in the Magical Dimension, where they enrolled in Alfea, a school for fairies. Reguardless of Bloom, Sonic, Spyro and the others being outsiders due to Bloom being rolled as a princess who was not coming to Alfea because Bloom was not on the admittance list and after Stella accidentally tells their friends that Bloom is actually from Earth while her misfit friends are heroes from other worlds, Alfea's Headmistress, Ms. Faragonda, allows Bloom and her misfit friends to stay because she is still a fairy and wishes to learn about magic.
Stella then introduces Bloom and her misfit possie some friends both new to Spyro's group and old to Sonic and Tails: Flora, who is a shy girl who loves nature, having nature-related powers and reminds Spyro of Fluttershy, an intelligent girl Tecna who she and Tails have a favorite in common: technology and she has technologically-based powers, Musa, a tomboyish girl who loves music and having musical powers, Sonic and Tails' pal, Knuckles, a red hotshot echidna with attitude, Sonic's pink hedgehog hammer weilding girlfriend, Amy Rose, Cream a sweet and kind rabbit with her friend Cheese the Chao, Sonic's lookalike and the Ultimate Lifeform, Shadow the Hedgehog, Knuckles' GUN agent rival and expert treasure hunter, Rouge the Bat, a battle robot named E-123 Omega and a trio of detectives, Espio the Chameleon, Charmy Bee and Vector the Crocodile who call themselves Team Chaotix. Bloom, Stella, Flora, Tecna and Musa form the Winx Club, the word "winx" being a pun on the word "wings." Eventually, Spyro begins to have visions about Bloom discovering her powers and has nightmares of his four new foes and new allies to the Villain Leage and the Syndicate of Darkness: a trio of witches Icy, Darcy and Stormy, who are students at Cloud Tower, an all-female school for witches and Sonic's arch nemesis and mad robot building scientist extraordinaire, Dr. Eggman who are after Magix's most powerful magic, The Dragon Fire and seven powerful gems known to Sonic that maybe the key to taming it, the Chaos Emeralds. All the while, our heroes befriend the girls' five student friends from Red Fountain, an all-boys school that trains them to become Specialists, warriors who can use a differing range of weapons along with other abilities. They are Sky, Brandon, Timmy and Riven.
During the season (Which is going to be made into a movisode), Dr Eggman and the Witches unleash constant traps to defeat Sonic, the Lougers and the Winx girls and get the Dragon's Flame. The turning point came in episode 17, when Bloom discovered that Brandon and Sky had switched identities in order to protect the other. Upset, Bloom returns to Earth, with the witches and Eggman secretly following. There, Bloom discovers her true identity - she is the princess of the planet Spark, and when it was destroyed by three Darkspawn Ancestral Witches who are loyal to Malefor himself, baby Bloom was sent to Earth by her older sister, Daphne, and was adopted by her Earth parents. Alas, the witches and Eggman attacked Bloom on Earth and took the Dragon Fire, leaving Bloom completely powerless. With the Flame in their possession, the witches used it to summon the Army of Decay, an endless darkspawn militia of insect monsters who regenerate when destroyed. At Alfea, the students struggled to fight them, but to no avail. Figuring the only way to defeat the witches is with a power equal to the Flame, the Winx Club, Team Sonic and the Louge travel to Sparx to claim any remnants of the Dragon Fire.
On Sparx, the Winx girls, Team Sonic and Spyro's group of Lougers are immediately attacked by vicious monsters, but manage to hold up in the ruined palace that once belonged to Bloom's family. Guided by the ethereal appearance of her sister Daphne, Bloom is told about final moments of her planet. After the destructive conquest by the three ancient witches to seize the Dragon's Fire, Bloom's parents, King Oritel and Queen Marion, endowed the infant Bloom with a small portion of it with some help of the chaos emeralds. She was handed off to her sister for safekeeping, while their parents used desperate measures to eliminate the witches. Oritel and Marion seemingly sacrificed themselves by using the full power of the Dragon Fire, rendering their planet inhospitable. Daphne supposedly used the last of her magical endowments to send Bloom to Earth. The bestiary of Domino eventually overran the palace forcing the Winx Club, Team Sonic and Spyro's lougers to retreat without any information on how to re-acquire the Flame.
The Winx and their friends proceed with a secondary plan to take it from the witches, who have now conquered Cloudtower and turned it into their base of operations. The Army of Decay quickly overpower the heroes and their specialist support, and they are once again are forced to retreat. While falling back to campus of Alfea, Daphne guides Bloom to a nearby lake where she appears and explains to her that the Dragon's Flame can never be taken from her. By sheer willpower, Bloom regenerates her powers with Sonic becoming Super Sonic to help her.
The final battle begins at Alfea, and with the Dragon Fire and the help of Sonic in his super form, Bloom squares off in a duel against Icy, while the others take on Darcy and Stormy. The Trix each have a share of the Dragon Fire, so when Darcy and Stormy are defeated, most of the monsters disappear, leaving only Icy to be defeated by Bloom. After the battle, the Witches are sent to the Fortress of Light, a temple, as punishment while Dr. Eggman escapes and a celebration is held back at Alfea. The Winx girls, their friends Mirta, Knut and the Specialists toast to the new year and the season ends with Spyro inviting Team Sonic and the Winx Club to help him reunite the abandon lougers after getting a tip from Ignitus that Kairi needs their help in London and the quest to bring the Louge's abandoned members back continues in Spyro and Tweety's High-Flying Adventure .