Rainbow S.r.l. offered the film to the Cannes Film Festival in 2007. Australian singer Natalie Imbruglia sings the film's theme song, "All the Magic". Elisa Rosselli performed the other songs, including "Fly", "You Are the One", "Enchantix, Shining so Bright", "Only a Girl", and "You Made Me a Woman". The movie was released on DVD in Italy in early March 2008.
Straffi has noted that it was difficult to animate the girls' hair correctly in 3D.
The story begins sometime after the third season with Valtor defeated and the magical dimension safe for the time being.
An unseen narrator begins to speak about a girl who discovered that she was a fairy and a princess: Bloom. Though her story is a magical one, it is one without an ending. The story will only have one when the girl writes the ending-i.e. creates the ending.
The scene changes to show six cloaked figures: the Winx. Bloom and her friends are on a search for Bloom's parents, King Oritel and Queen Marion which could change Bloom's life forever. The girls are on their way to find Hagen, a blacksmith who once forged the Sword of King Oritel. The girls successfully sneak into the castle but due to Stella's mistake, are forced to battle Hagen's robot guards. Fortunately, Bloom ends the battle by using her Dragon's Flame to destroy their power source. Hagen then holds Bloom at swordpoint in anger for the Winx girls trespassing his castle but Faragonda arrives in time to stop him.
At Alfea, Bloom, Hagen and Faragonda talk in her office. On Hagen's comment on the decoration of the school, Faragonda explains that some fairies are leaving the school to end their journey and become Guardian Fairies: All of the Winx except Bloom. Bloom then asks Hagen if he can sense the sword that he forged for her father, a sword that can never be separated from its master. Hagen states that he has been searching for the sword for years to find her parents but has not sensed it. Hagen tells her that she must face reality; her parents are not coming back.
Bloom, faced with the revelation that her dreams are over, runs off in tears and avoids her friends. She goes to the top of the castle where she watches the graduation ceremony. There, she befriends a small cat after she appears, whom she names Purr. Talking to her and Kiko, she explains that she feels that "the world has lost all it's colors, there is no more hope". Sadly, she sees her friends become Guardian Fairies (a form where they become strong enough to protect their planets) and graduate. Whispering that she loves them, she turns away in grief. Sky appears and comforts her.
Bloom is upset that all she and the Winx have done won't matter any more. Sky however tells her,"School might be over but life goes on." Riven also speaks to Hagen, asking him why he left the Company of Light. Hagen explains that they all have darkness and light inside them, the key is keeping the darkness in check. That night, there is a party and Bloom dances with Sky on the grounds. He encourages her to keep looking for her parents despite Hagen's words. Unfortunately, a ship arrives and Sky is forced to leave with a mysterious girl. As he goes, he promises that he will explain everything and never leave her.
Back in the dorm, the girls decide to remember the good times by partying together one last time. The next morning, Bloom leaves for Earth to stay with her adoptive parents for the time-being. Though she seems happy, Mike feels that Bloom is uncomfortable living on Earth. Vanessa agrees, stating,"This is not her world anymore." One night, Bloom sees in a dream what happened to her parents. Her father was pulled into another dimension by the Ancestral witches while her mother absorbed herself into the sword in order to be with him. Daphne then appears and tells Bloom that there is still hope; their parents are still alive. She gives Bloom her mask, telling her it will help her to see Domino before it was destroyed. She also tells her about the Book of Fate, a book their father kept that tells the history of Domino. Daphne gives Bloom its location before she vanishes, telling Bloom that she is not alone.
The restoration of Bloom's hope triggers the sword of King Oritel, deep within the Obsidian Circle. Its glow troubles the spectral forms of the Ancestral Witches, since they believed they destroyed all of Domino inhabitants. Obsidian's Keeper, Mandragora, appears before them asking for the power to escape Obsidian so she can search for the cause of the sword's reactivation. The witches agree.
In the morning, Bloom is surprised to see all her friends plus Sky there to celebrate her birthday. Bloom tells them her plan and they all agree to help her. They head to Domino where Bloom wears the mask and finds that Domino was actually a beautiful place before it was destroyed and covered with ice and snow. The group head towards the mountains where the book is hidden but Tecna tells them that a legendary bird named the Roc is guarding the library. The boys climb the mountain but thanks to Sky and Riven's arguing, the Roc awakens and flies off with the guys hanging on for dear life.
The girls run to the ship and manage to calm the bird with Musa's music and let it land. Inside the library, they meet Bartelby, Oritel's scribe in spiritual form, who shows them the Book of Fate. In it, they discover that Oritel as well as all the people of Domino are trapped in a horrible dimension called Obsidian. Bloom learns that she must travel there to free them. Wanting to learn more, Bartelby lets her turn the page but discovers jumbled words; the future has not yet been written.
Meanwhile, Riven is bitten by Mandragora's spy bug and becomes her puppet. Soon after, Alfea is attacked by Mandragora but the Winx, Mirta, the teachers and Faragonda are able to stop her. Bloom asks Faragonda to tell her more about Obsidian and learns about its cruel nature, how all the nightmares of the universe are within it. Just before they leave, Bloom looks at the Book of Fate and is shocked to see her parents wedding photo turn into a picture of her and Sky at the altar. Throwing the book aside in surprise, the picture changes into everyone fixing the school, which soon comes true.
The group head to Pixie Village where they enter the Tree of Portals. Only Bloom stays behind as she is not yet a guardian fairy and cannot miniaturise. Unfortunately, Jolly triggers an explosion inside the tree which causes the keys to become jumbled. Thankfully, Lockette finds the correct key and they all head to the gateway to the Obsidian dimension. As the girls enter, Mandragora appears and Riven begins to battle Sky. As he is about to stab him, Musa jumps in front of him and is injured. Riven sees what he has done and recalls all that they have been through together. He lifts her up and tells her that he now knows what he must fight for-her.
In Obsidian, the girls battle their greatest fears but survive. Next, Bloom sees a figure of stone that looks like her father. To her horror, the Ancestral Witches tell her that the figure is her father frozen in stone, the same fate as all inhabitants of her planet. The witches force her to make a choice between destroying the sword and saving her Earth parents or taking the sword and letting Mandragora kill them. Luckily, Bloom sees that in the image, her father is not sneezing as he pets Ron-her father is allergic to cats- and realizes that it is a trick. Sky arrives moments later and takes the sword but supposedly dies as he is not a king and only a king can take the sword.
Feeling all alone, Bloom is ready to give up when Daphne appears and reminds her that she is never alone. Bloom wears the mask and Daphne joins with her to destroy the witches. However, Mandragora returns and, using her body as a host, the Ancestral Witches begin to strangle Bloom. Sky stabs Mandragora with Oritel's sword, destroying her and the entire Obsidian Circle, freeing everyone and placing Miriam back in fairy form. Sky explains that he is now King of Eraklyon and that his coronation was the night he left Bloom at Alfea. Domino is restored and Bloom is finally reunited with her birth parents. There is a party afterwards where Oritel and Miriam promise Bloom that they will be around for the rest of her life. Mike and Vanessa are there too and Bloom hugs them affectionately.
Oritel begins the traditional father-daughter dance but lets Bloom dance with Sky. As the whole group dances, Sky swings by Brandon and Stella and takes a beautiful blue and silver box from Brandon. Moving away, Sky shows her a diamond ring. Leaning down, he whispers quietly to Bloom, asking her if she will marry him. Happier than ever, Bloom accepts and kisses him passionately.He preposes again in the second movie.
Bartelby then appears by the Book of Fate, telling the audience that the prophecy has been fulfilled and there is a new Company of Light- The Winx. However, the three Ancestral Witches have not been destroyed. Instead, they were freed and are finding new bodies to take over and destroy the Winx. They are shown with their descendants, the Trix, Icy, Darcy, and Stormy, cackling madly, which could imply that they have taken over their bodies.