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Z Is for Zenith
After Cedric swallowed Phobos, thus gaining the power of Nerissa's seal, he decides with Miranda to seek revenge on everybody. Cedric attacks Heatherfield and orders Miranda to destroy the Aurameres, granting her enough power to do so. W.I.T.C.H. and Matt leave for Earth. Regents of Earth enchant Heatherfield to prevent anyone from seeing Cedric or W.I.T.C.H. during the fight. C.H.Y.K.N., Elyon and Yan Lin's Altermere intervene and help W.I.T.C.H. to tap into their true powers. The girls each reach the zenith of their power, but lose their humanity in turn. With Cedric defeated, C.H.Y.K.N., Elyon and Yan Lin's Altermere escape, except Nerissa who becomes trapped in her own dream. Through the efforts of their friends, W.I.T.C.H. are able to get their humanity brought back. Elyon regains control of Meridian and returns to her throne. After the events, W.I.T.C.H. meets the computer teacher Pr. Raphael Sylla, who in reality is a hired mercenary planning to find out the truth of the Guardians and expose their abilities to the world.
Y Is for Yield
Final exams coincide with a test of cosmic strength, as the Guardians hold the future of the Universe in their hands. C.H.Y.K.N, Elyon and Yan Lin Altermere, who are trapped on the scepter of Phobos, attempt to contact Taranee to inform the Guardians that Caleb and Blunk are in danger. Will reveals her secret plot to defeat Phobos to everyone, including the recruitment of some of their former enemies to their side. Only just as things are looking up, a large twist interrupts things.
X Is for Xanadu
Phobos returns to Meridian and begins conquering it with his new powers. While the Guardians are trying to stop him, Hay Lin has to complete an art project on Xanadu, her vision of paradise. Meanwhile, she has also lied to her parents that Yan Lin left for a vacation in China to see distant relatives.
W Is for Witch
Phobos convinces the Guardians to release Cedric and Miranda for more protection. Meanwhile, as it is Halloween, the one night in the year when a Heart can be taken by force, the Guardians have to protect Napoleon, as he is Lillian's familiar. The race is on to keep Napoleon away from Nerissa, but thankfully the girls are able to walk around in Guardian form because of the holiday. Phobos tricks Nerissa and assumes control over her Seal. Meanwhile, Irma is forced to take her brother Chris, Lillian, and Blunk trick-or-treating, only to discover that her crush Andrew Hornby likes to trick-or-treat too. Irma gives Chris and Lillian a crash-course in how to get the most candy, using her own powers to help.
V Is for Victory
Will makes a deal with Prince Phobos, since only the heir to the Meridian throne can claim its Heart. Seeing as it has become part of Nerissa's power source, in exchange for freedom he is obliged to return the Heart. Will is having a rampage on Mandy at the swimming competition.
U Is for Undivided
Lillian is actually the Heart of Earth, its source of magic, and the Guardians have to protect her. Cornelia attempts to gain her sister's trust. Matt, Mr. Huggles, and Napoleon become the Regents of Earth. Cornelia is forced to babysit her sister while her parents are out for the night.
T Is for Trauma
Nerissa appears disguised as a student at Sheffield, but is soon uncovered and a battle ensues. The girls win by switching their enemies, knowing that element against element will only make them lose as the former Guardians have stronger powers and are more experienced. Hay Lin begins to wear braces on her teeth.
S Is for Self
Shagon manages to trick Will and makes her believe a lie. Nerissa deprives her Knights of their power to empower the old Guardians. Matt is free from Shagon and gains control. Nerissa traps Yan Lin inside her seal and decides to create an Altermere. K-SHIP decides to organize a battle of the bands.
R Is for Relentless
The girls try to protect Yan Lin, the last remaining former Guardian, from falling under Nerissa's control. Hay Lin and her grandma move from one dimension to another, trying to flee from the Knights of Destruction and Nerissa. Hay Lin has bad luck when her Fortune cookies haven't got fortunes in them.
Q Is for Quarry
W.I.T.C.H. pursues Nerissa and her Knights on Zamballa. They unknowingly falling in her trap, and lose Kadma and the Heart of Zamballa in the process. Will meets her father's girlfriend, Sarina Sanchez, and thinks she is Nerissa in disguise. Will hires Blunk to spy on Sarina.
P Is for Protectors
Nerissa and her Knights of Destruction attack Zamballa, a world of purple foliage with a populace of moving trees, disguised as the Guardians. When W.I.T.C.H. arrives to stop them, they are forced to fend off the Zamballians and their leader, Queen Kadma Starlighter, the former Guardian of Earth. Taranee starts to be angry about her mother.
O Is for Obedience
While Irma is trying to organize a concert for hit singer Vance Michael Justin, Caleb learns that Nerissa is his mother and confronts her in her hideaway at Mount Thanos. The girls struggle with Irma, who is giving them many orders to help organize a concert.
N Is for Narcissist
The Knights of Destruction attack the Fortress of Infinity, while Nerissa, posing as the Mage, corrupts Halinor Clarkson, the former Guardian of Fire. By accident, Cornelia receives the power of a Quinto Guardian, possessing all five elements, and Nerissa tries to use this to her advantage. W.I.T.C.H. must clean the cars and Will is reunited with her father.
M Is for Mercy
Shagon returns to Heatherfield as his old self, Matt, and keeps W.I.T.C.H. distracted while Nerissa corrupts Cassidy Chacon into joining her. Will stops being angry about her mother's and teacher's relationship.
L Is for Loser
Nerissa kidnaps Matt and Mister Huggles and adds them to her new Knights of Destruction, while Irma is faced with losing the friendship of her classmate, Martin. The radio station K-SHIP goes to Sheffield Institute. Members of the K-SHIP team are Irma, Martin, Uriah, Bess, and Courtney Grumper.
K Is for Knowledge
W.I.T.C.H. gains new knowledge of their sorceress foe Nerissa, a former Guardian and one-time holder of the Heart of Kandrakar. Will discovers that her own elemental ability to generate white-blue lightning and bring electrical appliances to life is Quintesence, which contains the very essence of life itself within lightning. In the subplot, after Taranee's mother forbids her from seeing Nigel, Taranee decides to turn herself into a bad girl to rebel.
J Is for Jewel
The Guardians are divided, each of them on family vacations, but Hay Lin is the only one left at Heatherfield. The Knights of Vengeance attack Phobos's prison and manage to free their prince, and it is up to the Air Guardian to gather the girls so they can fight back. Meanwhile, Elyon wishes to know about her parents, and after giving her lies about them, Trill reveals herself to be Nerissa, and traps Elyon inside the jewel from Queen Weira's crown she'd given her earlier, stealing her powers and kidnapping Elyon. In the subplot, Hay Lin meets and falls head-over-heels for a boy named Eric.
I Is for Illusion
The girls go on a vacation with Irma's family. They are having a rough time adjusting to living in a cramped space, but they manage to cope until the girls begin acting negatively to one another. At one point they get into a potentially dangerous situation, and the result ensues in an all out argument. The Oracle then appears to them, asking to claim back the Heart because of distrust and absence of harmony amongst the girls. Only Hay Lin sees the shadow of Nerissa cast by the Oracle, and the girls know there is something wrong. A battle ensues, and Caleb and Blunk return from Meridian in time to help out and victory goes to the Guardians. The girls then apologize to one another and stop arguing. In a subplot, Caleb and Blunk are fighting against the other Knights of Vengeance.
H Is for Hunted
Will creates an Astral Drop of herself so she can get her chores done. Nerissa then turns it into an Altermere, an exact duplicate of Will, including her feelings, memories, and powers. While Will is trying to find it, Nerissa convinces it to take Will's place, and a battle erupts. The other girls try to help, but they can't tell which Will is real. The Altermere becomes good and is almost destroyed by Nerissa but Will absorbs it into herself in order to let its feelings, memories and emotions "live inside Will's mind." In a second storyline, Will is forced by her mother to do laundry.
G Is for Garbage
Blunk finds another Horn of Hypnos, but it gets stolen by Jeek. Irma leaves for Meridian along with Matt and Blunk. The three track Jeek's hiding spot, only to find out that the Knights of Vengeance took the horn. Irma has to work with Blunk to save her friends, as they find out Matt and the other Guardians have been turned into Trance Marchers. When Will blows the horn at Irma and Blunk, they fake being hypnotized to get close enough to the horn to destroy it. Irma is mad at Blunk for covering her garage in garbage. She is grounded and forced by her father to clean up.
F Is for Facades
Disappointed at Caleb because of his decision to stay on Meridian, Cornelia goes on a date with Taranee's older brother Peter, disguised as her 'older' sister Lillian. The other girls follow, Elyon, Caleb and Lillian included. Meanwhile, Caleb swallows his pride and tries to ice-skate for Cornelia despite his lack of skills. Only they are interrupted when a distress call is heard from Meridian: The Knights of Vengeance have captured Drake, Aldarn, and his father, Julian. After the team arrives at Meridian, Caleb and Blunk are captured. W.I.T.C.H. arrives to save them, and momentarily the girls believe Caleb and Julian to be gone. After realizing how upset she was without Caleb, Cornelia decides to break up with Peter and return to Caleb. During this episode, Cornelia reveals her power of being tall and Irma reveals her new ability of changing the colors of clothing.
E Is for Enemy
While the girls are experiencing frighteningly realistic dreams, a new dilemma appears: Will's mother plan to be transferred from Heatherfield so she and Will can start over someplace else. As the girls stake out in Susan's office building to destroy the transfer request, the girls fall asleep. While asleep,some of them fall asleep next to one another and experience the same dream. Taranee determines that the dreams are the result of someone's interference, and all sleep next to one another to fight in the dream together. The girls find out Nerissa is to blame and defeat her while in the dream. The girls then convince Will's mother to keep Will in Heatherfield.
D Is for Dangerous
W.I.T.C.H.'s new foe Nerissa creates beings known as Annihilators and sends them on a rampage in Meridian while Elyon is on Earth. Will defeats the Annihilators with an unknown lightning-based power she is gradually developing, in addition to bringing electrical devices to life. While Matt convinces Caleb to train him to become more useful to the group, Mr. Huggles escapes from his cage and creates chaos in the Lin's restaurant. Hay Lin gives Mr. Huggles to Taranee, but Taranee's father has an allergy to fur. Taranee then passes Mr. Huggles to Cornelia, only Lilian frees Mr. Huggles to meet Napoleon, and more chaos ensues. Cornelia finally gives Mr. Huggles to Elyon, but Mr. Huggles escapes again and returns to Matt where he stays permanently.
C Is for Changes
The Guardians are taken by surprise by their new powers: Will can bring electrical appliances to life, Irma now can use mind control, Taranee now can use telepathy, Cornelia now can use telekinesis, and Hay Lin can become invisible. The Knights devise a plan to blackmail the Guardians using Elyon's disappearance to make Earth authorities and their parents suspicious of their recent activities. After things are cleared up, Elyon decides to finish the rest school year, Caleb accompanying her. Meanwhile, Will is grounded because her poor grades and her mother sets her to transfer schools.
B Is for Betrayal
The Knights of Vengeance attack Meridian and begin targeting those who betrayed their former master. Back on Earth, Will gives Cornelia a cat, but Cornelia gives it to her younger sister Lillian. Just before Lillian names the cat Napoleon, the Guardians are called to another realm, Kandrakar, and learn of their new status as the Guardians of the Infinite Dimensions, after the Veil's lifting. In the subplot, Cornelia and Caleb are having relationship problems. The girls also notice a sudden change in Cornelia's powers, and Cornelia develops a crush on Taranee's older brother Peter.
A Is for Anonymous
While everyone is celebrating Phobos's defeat, a kitchen worker named Trill gives the newly crowned Queen Elyon a jewel what belonged to her mother, Queen Weira. Caleb reveals to Cornelia his intentions to stay in Meridian and serve Elyon. Taranee starts thinking she will turn into an "invisible girl" again, and begins to act up at school. The Guardians are faced with an old enemy, Frost the Hunter, who followed them to Earth. Frost kidnaps Irma, Cornelia, and Hay Lin and threatens Taranee to bring Will to him without Heart of Kandrakar. In a subplot, a new foe called Nerissa appears. She frees Miranda, Gargoyle, the Tracker, Sandpit, and Raythor. Miranda betrays Phobos and does not free him. Nerissa and the others meet Frost. Now the enemies who Nerissa released are called Knights of Vengeance.