The Winx continue to try defending the Cloud Tower School for Witches from the evil Trix. However, the Winx are split up, and each girl's weak points are revealed. Then the Trix find a way to control Cloud Tower itself and work for them drawing them closer to the Codex.
The wait for the container to open finally ends and Griffin is seen standing at the opening of it, which surprises everyone. Icy wants to know what is happening and Griffin sarcastically congratulates them for finding her "spa". Clearly, this is not the Codex room. This realization angers the Trix after they had wasted their time.
The Trix prepare to fight Griffin but because they are outnumbered they escape by having Darcy darkening the room. After the Trix are gone, at least for now, everyone turns their attention to Bloom as she had been knocked out and blinded by the Trix.
Bloom's vision is restored thanks to Griffin but she feels horrible. Stella scolds her and Bloom comes to understand that what she did was very risky. Tecna expresses her own guilt because if she had not tried to search for the Codex, her friend would not have gotten hurt.
Elsewhere in the school, away from prying eyes, the Trix find another alternative to steal the Codex. At first they are irate that Griffin and the Winx are working together to guard the Codex but realize if they were to separate the Winx, they could probably win.
The next morning, the Winx, Lucy and Mirta are given ruby coins that were made by Griffin. These coins detect the use of a spell that controls Cloud Tower and therefore, allows the group to track the Trix's movement. Griffin explains that she had discovered the Trix are moving about the school with help from Cloud Tower itself. And so these coins will help track them. She also taught them a communication spell that allows them to communicate solely through the walls of Cloud Tower. After that, the Winx, Lucy and Mirta are all ready and begin their mission. The Trix were spying on them, and now that their enemies have split up, they intend to keep it that way.
As the team start their search, Griffin goes around to check up on them, with the first being Flora, Aisha and Zing. And at some point, Mirta and Lucy. Strangely though, Griffin is at her office and was preparing to enter mediation to regain complete control over Cloud Tower. Zarathustra then asks if she purposely sent the fairies to keep the Trix busy. Griffin rejects such dangerous act which prompts another question from Zarathustra, why did she split the girls up and with their polar opposites? Griffin simply answers that it will either strengthen or damage their bond, whichever one it is, they will learn from this experience. She then proceeds to her mediation room.
Mirta and Lucy continue walking down the hall, when Lucy tells Mirta that it is okay to call for the Winx when they need help. Just then, Griffin appears again, which spooks them and when Mirta wonders if she is here to check up on them again, it is revealed that this Griffin is really Darcy in disguise.
Tecna and Bloom had entered a classroom sometime ago and Bloom complained that walking around will not make the search faster. She looks at Tecna aware that she may have some ideas on how to search faster. Tecna intially refuses to use technology to search for something again as she still feels guilty. But Bloom thinks there might be a technical charm they could use. Tecna agrees and once she logins to her device, she places the coin atop of her technical charm spell. The only disadvantage - no detection system until the spell is completed. Musa and Stella have entered the cafeteria but they clearly have other ideas of what they should do which causes them to bicker and Stella accidentally dropping the coin
Meanwhile, Flora and Aisha plan to team up with Mirta and Lucy but when they tried to contact them, no one answered. And eventually, Tecna completes the spell and reports to Bloom that the Trix are within proximity and more precisely, in the cafeteria where Stella and Musa is. Bloom quickly uses the communication spell and as she calls out to them she hears battle cries, realizing they were too late. Stella and Musa remain trapped in the walls of Cloud Tower.
Unsure of what to do, Aisha decides that it would be best if they meet up Bloom and Tecna. Bloom also wants to inform them about the situation on their end and they communicate to each other about meeting up in the classroom. The witches are now dealing with a problem of their own, fleeing from their own school! The Trix are using Cloud Tower to trap the witches, making it easier to deal with fewer people. The remaining two witches, one of them being Shilly, manages to find Bloom and Tecna to relay the emergency. As they converse, Bloom and Tecna start to bicker a bit and then realize that they had stepped away from the monitor and it becomes too late as the Trix find and taunt them. The two witches then leave the room for safety.
They transform and battle, during which Tecna's leg is injured. Out in the hall, Aisha, Flora and Zing hear these battle noises. At first the two were too frightened to quickly come to their aid but eventually proceed. Bloom and Tecna then flee the room aware that they are no match for the Trix. Luckily, before the Trix could get to them, Griffin regained control over Cloud Tower the last minute and trapped the Trix. Having enough of Darcy's old "control everything" way, Stormy suggests chaos to escape.
The Winx are able to regroup afterwards, and Griffin finally frees Stella and Musa. Griffin now goes to help her own students and tells the fairies to stay together. The Winx then walk around the school but because the Trix is really using brute force, the school is going crazy. This causes a crevice to open below the Winx and they fall in. The Trix are then able to escape the school at last but now Darcy wonders where the Codex is. Icy looks up and realizes that the Codex could be in the spire and they proceed to check it out. Meanwhile, the Winx have trouble finding a way but they eventually realize where the Codex is and try to get outside.
The Trix locate the Codex first and Icy breaks open the structure. Discorda greets them and tells them to scram as she is the Guardian Pixie of Cloud Tower. Before the Trix could do anything, the Winx interupt them and well aware of the Trix's power, they begin their convergence spell. Should they finish the spell, the Trix will be overpowered but because they did not decide what the spell should do and there is no harmony amongst them the spell backfires. This in turn gives the Trix the advantage, they overpower Discorda, steal the Codex and then leave. This now makes Darkar more powerful and the good in even more danger.
- Total Darkness - Used by Darcy to darken the room.
- Sunbeam -Used by Stella to illuminate the room.
- Heat Wave - Used by Bloom against the Trix.
- Gloomix Perfect Storm - Used by Stormy against Bloom.
- Perfect Storm - Used by Stormy against Tecna and Bloom but failed.
- "Liberato" - Used by Griffin to free the captured Winx and witches.
- In this episode, Zing makes cosplays of Aliens, Jack Sparrow from Pirates of the Carribean, and Doc Holliday from Tombstone.
- In the original version, Bloom's and Tecna's transformation marks the last appearance of the initial Winx transformtaion scenes where the Winx wear their Season 1 civilian outfits. Those scenes were no longer used in the later episodes since the Winx's everyday civilian outfits were changed.
- However, the 4Kids version kept using these scenes despite the winx wearing new outfits.
- In the beginning of the episode, the witches are behind the Winx but once Darcy darkens the room and Stella brings light, they are gone.
- Musa is missing her midriff at one point.
- When Stella and Musa are stuck in the wall, when angled at Stella, Musa's pants are gone.
- When Bloom grabs on to the door handle before the door disappears it is blue, but when it reappears it is red.
- There are times when Icy laughs, her makeup is gone.
- Bloom's sleeves are missing in one scene.
- As a group of witches run away from their school's attacks, Shilly and another witch (who looks exactly like Darma) remain and run to find Bloom and Tecna. When they arrive, Endora replaces the other witch even though she was the first to be trapped.
- Stormy's arm glove becomes a complete glove after she confronts Discorda.
- There are times where Stella is missing her armbands.
- There are times where Flora is missing the highlights on her bangs.
- Flora's earrings are outlines at one point.
- Icy's Gloomix's diamond is colored in with a blue color.
- After Mirta checks up on Lucy, her wristbands are missing.
- When Aisha blinks after trying to contact Mirta and Lucy, her eyes are completely white.
“It will either strengthen their bond or destroy it. One way or another, they'll learn something.”
“It's just that... If we do run into trouble and you wanna call the Winx for help I... won't get mad.”
“It's a sad day for all who live.”