The episode begins with Caleb's voice over narration of the fugitive rebels' plight ever since the Infinite City has been taken. With Elyon's coronation only one day ahead, the rebel leader needs to form a plan for crossing the treacherous Meridian Plains unseen. But his thoughts are interrupted by Yan Lin's intervention. Yan Lin worries about Matt's discovery of the Guardians' secret, but Will reassures her by saying that Matt knows Elyon from school and wants to help. While Hay Lin is feeding the dormouse Mr. Huggles in his plexi-tube hamster habitat, she comments that it's a pity the rebels don't have such a tube under the castle to sneak through. This causes a lightbulb moment for Caleb who decides to use multiple portals to create a shortcut in reality. The rebel army will transit through a Portal on Earth and Will will open another Portal right next to it so that the rebels can then to cross directly into the castle. Blunk offers his help but Irma hurts his feeling by replying "Face it dude, you're not a warrior, you're a scavenger."
In Meridian Elyon's powers have finally reached their peak. She's excited about the coronation the next day, unaware that Phobos and Cedric have made some "arrangements". At the bottom of the castle Cornelia uses her Earth powers to clear a path through the vines into the Abyss of Shadows for Will, Caleb and herself. Once inside, the Guardian leader opens a Portal leading out into the kitchen of a deserted Heatherfield model home. Having found a secure location on Earth, Will creates a second Portal back to Meridian which opens onto the Hoogong Gorge.
Meanwhile a blissfully oblivious Elyon is summoned to the throne room for what she thinks is a "rehearsal". But Phobos tells her there's been a slight change in plans: the Coronation isn't tomorrow morning. It's going to be tonight. When Elyon disbelieving asks why, Phobos replies "In case any kind of attack was being planned to save you." And before the Princess can fight back, vines grow out of the throne's arms and grab her, pinning her to her seat. Roaring, Cedric morphs into lizard-mode before her eyes. Elyon, horrified, powerlessly strains at her restraints and screams.
The second acts opens at the Silver Dragon where Caleb is snacking: "We cross the Veil for the assault on the castle in twelve hours. I need all my strength." Little does he know that Matt has also taken his parents to the restaurant with the covert intention of checking up on Will. When he sees Cornelia and Will rush into the kitchen he excuses himself from the table to go eavesdropping. The Earth Guardian is telling the others that she has a "horrible, overpowering feeling" that Elyon is in danger right this moment. Will trusts Cornelia's instincts and decides to move up the attack.
Elyon is still a prisoner of the thorny throne and when she asks her 'friend' Miranda for help, Miranda morphs into the beast she has been all along. In the meantime W.I.T.C.H. meets up with the rebel army at the Hoogong Gorge and leads the troops through the Portal into the Heatherfield kitchen, then through the second Portal into Phobos' castle. Cornelia and Caleb are the last ones to cross the Veil and just before they do Cornelia gives Caleb a long-delayed kiss. Right when the troops are ready to launch the assault, they are ambushed by a group of castle guards. Thankfully it turns out that the guards have been convinced by Tynar to switch to the Guardians' side and fight alongside the rebels. Unbeknownst to them all Phobos has already begun the power transfer to drain his sister of her magic.
Meanwhile on Earth Matt has arrived at the model home after following the girls from a distance. He literally stumbles upon Blunk who takes him across the Portal. While Will frees the slaves working in Phobos' kitchens, Cornelia heads for the throne room where Phobos has just been informed of the rebel assault. He and his entourage storm out to bawl into the fray, leaving Elyon alone for the Earth Guardian to save. Matt also comes to the rescue but it's Blunk who actually saves Will, Taranee and Hay Lin from Cedric's attack by biting his tail and screaming proudly "Not just scavenger. Warrior!".
Will flies Matt away, only to be confronted by Phobos who is putting his new powers to good use. Furious because Cedric has "failed for the last time", the Prince reduces the giant Snake-Lord into a tiny snake, then rounds on the Guardians. At first he appears unbeatable, but the tide turns when Elyon makes her entrance and wields her remaining magic so she and W.I.T.C.H. can defeat Phobos together. He summons the might of the Emperor's four dragons to fend off the girls' attack, but to no avail because the power of the Heart of Kandrakhar cannot be corrupted. Elyon traps him in an energy cage and sends him off with a "Goodbye, Phobos. You were never my brother." Cedric and Miranda are teleported away along with the Prince and the rebels cheer victoriously.
Elyon's restored magic transforms her Kingdom into a paradise. She is now Meridian's Queen and acclaimed by her people. Cornelia and Caleb happily hold hands and Will and Matt soon follow suit. Yan Lin instructs The Mage – who is to act as Phobos' warden – to guard him very carefully: "A tyrant who has tasted power is twice as dangerous." The Guardians celebrate and Will rejoices that "all is over", but in the Infinite City below The Mage joins Phobos and his imprisoned goons and enigmatically comments that "Now it all begins."