The three Trix, Stormy, Icy and Darcy, return to the Cloud Tower School for witches. The Winx must enroll at Cloud Tower to help protect it against evil. They have no luck working together with the witches, and the Cloud Tower aura of discord even turns the Winx against one another.
Faragonda speaks with Griffin in her office about their students working together to prevent the Trix from stealing the school's Codex. Griffin is not pleased with working with fairies but sees that there is no other choice. With the agreement in place, Faragonda sends the Winx to Cloud Tower to provide extra security for that school's Codex piece as she and Griffin believe it to be Darkar and the Trix's next target.
Mirta joins the girls on this mission as she was a former student there and therefore, the perfect guide. When they arrive, the professors Ediltrude and Zarathustra greet them at the entrance but it is clear that they dislike the fact that they are here. The professors escorts them into the school but not before correcting Bloom's comment on the school being "a building". The two explain that the school is in fact, a living being created by ancient witches (much to the disgust of Stella). As they are escorted into the school, the Trix appear above the school, ready to start their own mission.
The Winx then start their first lesson in witchcraft and they can feel the uncomfortable aura set in place by the witches as they stare at them with dissatisfaction on their faces. The Winx also learn about the witches' source of power, how they work and their constant urge to betray one another. Meanwhile, Mirta goes to her former dorm room and knocks on the door. When Lucy does not answer it brings tears to her eyes, and so, she walks away.
In class, the Winx and the witches perform their exercise - conjuring a sphere of magic forged through dark feelings and emotions while subduing light. Griffin goes around the classroom, providing critique on her students' progress. Some of the witches had some bad outcomes with the spell, Musa is doing rather well (much to the surprise of Griffin), and as usual, Stella just does her own thing by changing her dark sphere into light. Bloom on the other hand is exhausted from doing the spell, a fact Griffin notes as it is not easy for fairies to easily summon negative feelings.
Elsewhere in the school, Stormy gets angry with their lack of progress in locating the Codex. She blasts a display containing glass which prompts her sisters to scold her as the noise she is making could attract their enemies' attention. They then decide their next course of action: split up and search. While Darcy and Icy create a hole through the wall to go to different areas, Stormy steps outside of their hiding place and sees Mirta walking down the hall. She discreetly follows her knowing that she will lead her to something useful.
In another room, the Winx and witches (including Lucy), are in a serious discussion about preventing the Trix from getting the Codex. Both sides remain on the bickering, uncooperative end until Mirta steps in and reminds the witches of what Griffin could do to them if the Trix win due to their lack of cooperation. And with some encouragement from Bloom the opposing ends supposedly join forces. As they celebrate their collaboration, an eye appears in the wall. The eye spies on them and allows Stormy to see what the Winx and her former classmates are up to. Icy sees this and she decides to go get Darcy because she sees a very useful weak link amongst the group.
In Lucy's dorm room, she and Mirta catch up and reminisce about their good old days leading up to their present day. Mirta also jokingly hoped to convince Lucy to become a fairy as well. Lucy refuses and proudly states that if she continues to study witchcraft she will gain even more power. When Mirta remarks how Lucy's goals have not changed, Lucy is quick to defend herself and the other witches declaring that they are not all evil like the Trix. Lucy also mentions her newly found role model - Griffin. The girls finally make up even though they no longer attend the same school and are in retrospect, on opposing sides.
Though this happy reunion comes to end when Lucy walks down the hall only to be stopped by her former bullies - the Trix. Lucy does her best in trying to defend herself against them when they try to coerce her into helping them. When that did not work and Lucy had attacked Icy, they magically threaten her and as a result, the terrified Lucy reluctantly helps them spy on Griffin and Ediltrude.
As Lucy eavesdrops on Griffin and Ediltrude's conversation in Griffin's office, Griffin is pleased to see that her students and the Winx are cooperating and checking for all possible hiding places of the Trix. When Ediltrude almost mentions the location of the Codex, Griffin immediately stops her and magically make her office door disappear, revealing Lucy. Frighten, Lucy runs away and when Ediltrude tries to chase her down, Griffin reasons with her as it is clear that the Trix forced Lucy into this.
When Lucy, in her frightened state, tries to call out to Icy she is spooked by Zing. Lucy runs away and sees the Winx and Mirta outside their room. She eventually succumbs to her fears and faints. Mirta checks up on her and a dazed Lucy tells them that the Trix are here in the school. With this information, Bloom tells her friends that they need to go search for them while Mirta stays with Lucy.
The Winx start running down the hallway but with no lead or direction. The girls spout out different ideas and Stella is clearly annoyed that no one is thinking this through, everything is mess and no one is listening to her. She decides to break away from the group to cool down. The girls then split up. Bloom and Flora goes somewhere, Tecna believes that she has the best solution in locating the Codex room and goes to sit in another room to focus on that, and Musa and Aisha search elsewhere.
After fiddling with her PDA, Tecna is able to locate the school's Codex room. But before she could report this to her friends, she is ambushed by the Trix and is frozen in ice by Icy. The Trix now know the location and proceed to that room. Meanwhile, Musa and Aisha find a room with a completely different vibe, tall statues and a group of witches. They proceed to question them. The Trix themselves are having a difficult time getting to their destination because they cannot go through the walls as easily due to having no control over the school. So, they try a different tactic - forcing their enemies to give them what they want.
After hearing the commotion, Flora and Bloom run into the room Tecna is in and sees what the Trix had done to her. They realize Tecna had found the Codex's location and the Trix learned it through her. Bloom tells Flora to stay with Tecna while she goes after them. Flora then finds Stella to help meltdown the ice and free Tecna.
After questioning the witches, Musa and Aisha still do not believe their words and they continue to insult and bicker with each other until the Trix enter the room. The fairies and Cloud Tower witches try their best to stop the Trix from getting closer to the Codex, and since they are wasting their time, the Trix decide to make the statues defend them. Now, the witches and fairies have something else to deal with as the statues begin their assault, while the Trix go get what they are looking for. Bloom is the first to find the room the Codex is in and transforms to be ready for the Trix.
The witches, Musa and Aisha were able to destroy the statues but at the cost of letting the Trix get away, and although Tabitha praised their teamwork, Musa and Aisha are still on the defense and ridiculed them for letting the Trix escape. Offended, the witches argue back and they proceed to fight one another until Flora, Stella, Tecna and Zing enter the room to stop them because the Trix are headed to the codex room and Bloom is all alone by herself.
They proceed to run towards the room and when they arrive Bloom had already lost the battle with Trix by being blinded by Darcy. And the Trix are about ready to get their codex once the container opens...
- The Winx Club go to Cloud Tower with Mirta to act as added security for that school's Codex.
- Mirta and Lucy reconcile.
- Glacial Sleep - Icy used it to freeze Tecna.
- Sonic Vibe - Musa used it against Icy's attack.
- Blast Ball - Bloom used it against the Trix.
- Optical Darkness - Darcy used it to blind Bloom.
- In the 4Kids dub due to a numbering mix-up, this episode was aired after "Magic in my Heart". When released on DVD, this was fixed.
- In the 4Kids dub, Kether Donahue (Candice in Pokémon DP Galactic Battle) had a guest role as one of the witch students of Cloud Tower, Hecate.
- The part where Musa was being chased by witches from "Betrayed" was used for this episode to recall Musa's bad time with witches.
- Stella continues to be a delinquent, even when not in her own school. She does not care if she fails her classes in Cloud Tower, as she admits to having a bad permanent record anyway.
- Zing cosplays as:
- In the 4Kids version, Faragonda sends the Winx to Cloud Tower to learn about Dark Magic.
- When Icy froze Tecna, her pose was similar to Bloom's when she first encountered the Trix in Magix and Icy froze her.
- Faragonda is missing her lips when the Winx express their shock at being sent to Cloud Tower.
- Bloom's Winx form's gem is on her shirt when she and her friends nod.
- In some scenes, Flora’s earrings are outlines.
- When Musa comments on their embarrassing situation, Bloom is missing her sleeves.
- There are times in which Flora's highlights on her bangs are missing.
- In one scene, Aisha's eyes are colored in.
- As Bloom's ask Griffin if she could be dismissed after completing the spell, Flora is missing.
- Lucy mentions that Bloom actually gave the Trix one piece of the Codex. This does not happen until "The Spy in the Shadows".
- In one scene, Bloom's wings went missing when the Trix attacked her.
“Umm, the witches think that Alfea fairies have it easy. And all the teachers say that fairies wouldn't last two days if they were to take their classes!”
“Ever since we got here the witches have done nothing but stare at us!”
“They're just jealous of our sense of style that's why!”
“Team members can betray one another, that's why a witch depends on no one but herself!”
“Many of our spells require darkness as a primary source of energy, so it's important to learn to subdue light.”
“Okay everyone, this is our chance to stop the Trix before they get enough power to threaten all the magic dimensions! Let's make Griffin and Faragonda proud!”
“Hey! Not all witches are like the Trix! Lady Griffin is strong and proud and someday I'll be just like her!”