A new trimester starts and Sakura is now a fifth grader. She walks to school with Yukito, who gives Sakura a watch as a late birthday and start of fifth grade present. Sakura's new homeroom teacher turns out to be Ms. Mizuki. Sakura looks out the window and thinks she sees cherry blossoms, but realizes it is snow. Later, the snow is piling very quickly, even though it is April. It turns out to be the doings of a Clow Card. Sakura with Tomoyo look down at the snow-covered city to find the card with the Fly card. They stop at the big penguin at Penguin Park where Syaoran and Meilin appear. Syaoran tells the group that it is the doings of the Snow card. Suddenly, a blizzard surrounds them and it appears to be following people with magical powers. Sakura tries to use the Fly card to get herself, Kero, and Syaoran away from the blizzard. Syaoran uses a fire spell to try to stop the blizzard from following them, but it just becomes more furious. In the middle of the flight, Sakura realizes the watch she got from Yukito is gone. Sakura gets angry and releases the power of Firey to burn all the snow and captures the Snow card. Even though Sakura caught a card, she cries because she lost Yukito's present to her. Kero leaves Sakura and Syaoran to get Meilin and Tomoyo. Ms. Mizuki appears and gives Sakura the watch she lost and Sakura thanks her, while Syaoran glares at Ms. Mizuki.

Sakura and her friends are at a picnic with a portable karaoke device Tomoyo got from her mother's company. It is Tomoyo's turn to sing, and she begins singing. The next day at school, Sakura and Tomoyo talk about the song that Tomoyo will sing in choir. At cheerleading practice, Sakura, Chiharu, and Naoko talk about Tomoyo's singing, and decide to go listen after practice. However, Tomoyo's voice is stolen by a Clow Card. Later that night at Sakura's house, Kero tells Sakura that the Voice card caused this. Sakura and Syaoran go to Tomoyo's house to try to seal away the Clow Card. Then, Syaoran and Sakura begin thinking of ways to capture the Voice card. After a comment by Sakura about the Song card, Syaoran comes up with the idea as using the Song card to sing with Tomoyo's voice to draw out the Voice card. It works and the Voice card comes into Tomoyo's house. Syaoran seals the exits with seals, so that the Voice card cannot escape and Sakura seals the card. Tomoyo's voice is returned to her, and she is able to sing in the choir. Sakura and her friends go to the concert and listen to the choir's singing.

The challenge is over at last. All the cards have been captured, all have been turned. The tests are over, or are they? There may be just one remaining, one that may have to be resolved with the heart. Life has been difficult for Sakura and Li since the day Synoran confessed to sakura that he was in love with her, Li finds it difficult to approach Sakura, whilst Sakura herself is torn, not knowing if she feels the same way for Synoran. The two barly exchange words when they return to school, where they are told by Tereda-Sensi that Eroil is transferring back to England. Sakura, Li, Tomoyo [Armed with her camera as always] and Kero head for Eroil mansion, seeking answers, they are startled when the mansion's front door opens by itself, as do all the other doors from within the building. When the final door opens, the four are shocked to discover that Eroile is holding a party for them!

On her way home Sakura bumps into a woman in the street. After arriving at school the next day, Sakura discovers that her math teacher will be on extended vacation and the replacement is the woman she bumped into the day before, Ms Mizuki. During the lunch break Syaoran reveils to Sakura and Tomoyo that the substitute has a strong magical presence and that they should be careful around her. When school finishes Sakura and Tomoyo go to a shrine to pick up a romance charm. Upon arriving Sakura feels a presence. While at the Shrine they also see Meilin and Syaoran. After a brief conversation they are all transported into a labyrinth, it is soon discovered that this is the work of the Maze card. A number of escape attempts using the Fly and Sword cards are foiled. The Maze then starts to change shape and Meilin is separated from the others. While searching for Meilin, they find her with Ms Mizuki and they soon escape the labyrinth with Ms Mizuki's help. The Clow Card is then captured, however it goes to Ms Mizuki who promptly goes on to give it to Sakura.

Christmas is coming, which is also Yukito's birthday, but Sakura is unsure what to get him. She asks Meilin for advise who tells her it can anything because if the person likes her they will like the gift. Sakura asks Yukito to go to the amusement park with her, using tickets given to her by Chiharu. Tomoyo and Kero follow them to film Sakura's "date". Sakura and Yukito run into Syaoran and Meilin. While they are at a cafe, the Firey card appears. Syaoran uses the Time card, giving Sakura time to use Sleep and put everyone at the park asleep. She then tries to capture Firey using Windy, but Firey is a strong attack card and Windy is unable to defeat it. Sakura has to use two elemental cards, Watery and Windy, together in order to capture Firey. With Firey captured, Kero regains a small amount of his power, enabling him to make small fires. Sakura gives Yukito his Christmas present: a doll of himself.

Syaoran's feelings for Sakura have been steadily increasing, though he still doesn't understand why, and Sakura remains blissfully unaware of it. Soon Sakura invites him to go to a teddy bear festival with her, Tomoyo, and Eriol. However, Eriol secretly traps Sakura and Syaoran on an elevator, where the two grow closer. Eriol then creates a large hole in the wall of the elevator, causing Sakura to fall through. Distraught, Syaoran calls out to Sakura by her first name for the first time.

Eroile stands above Sakura, Synoran, Kero and Tomoyo, and reveals the truth at last: He is the reincarnation of Clow Reed himself! He then casts a spell that eclipses both the sun and the moon. This puts those not entuned with magical power to sleep. As Yue and Toya race to the shrine, Toya collapses, with no power to call his own any more, the spell is able to affect him also. Eroile then challenges Sakura to use her abilities to break his spell of Darkness or everyone will sleep forever! With Kero and Yue being kept busy by Spinal Sun and Ruby Moon, Sakura knows she is vulnerable, so she strikes quickly. She uses the shield card to protect Synoran and Tomoyo and uses the jump card to get closer to Elrole, but the sorcerer summons a fire spell to drive her back, Skaura falls backwards, Synoran uses wind magic to catch her, but in doing so, drains himself of all his remaining strength. After further battle, and more card changing, Sakura realises that only the power of light can shatte

It's April, the cherry trees are in full bloom, and Sakura has entered Tomoeda Middle School. She's reunited with Syaoran, who has returned from Hong Kong, and her new student life has begun.

Sakura has the same recurring dream she had in episode one, specifically focusing on the boy wielding a sword in Chinese clothing. She hears from both Cerberus and Yukito that it might be a "foretelling dream". A new transfer student arrives from Hong Kong named Syaoran Li and is seated behind Sakura. He terrifies Sakura with his glares all day and during recess, he demands Sakura to give him the Clow Cards. On the way home, there is a lighting storm, but no rain. Cerberus explains Syaoran is from the Li clan, a famous family of Chinese sorcerers from which Clow's mother came. The same lighting storm for earlier appears and Sakura deploys to battle the Thunder card. Syaoran demonstrates his command over elemental magic and calls on thunder god to return the Thunder card to its original form. He instruct Sakura to use the Shadow card to encage the Thunder card so it could be captured. Thanks to Syaoran's constant derogatory remarks, Sakura is left feeling upset after a card capture for the first time.

During an attempted card capture, Kero and Syaoran were holding down a card (CHANGE) that took form of an animal. Sakura turned it back into a card, but because they were both touching the card at the same time, Kero and Syaoran swapped bodies. Kero tried to make it though a day as Syaoran without anyone noticing, but didn't do very well. At the end they finally change back when Sakura used the CHANGE card.

Rain still falls on Tomoeda. In her kitchen, Sakura thinks about the previous night when she was unable to release her key into the staff. Touya comes downstairs and notes that she's up early as well as calling her a monster, but is visibly concerned when Sakura makes no retort. She asks him if Yukito was going to visit their house that night and he tells her that Yukito hadn't planned on it, but that he would probably come if they were having something good for dinner. In Sakura's room, Kero thinks about the strange presence he sensed the day prior, hoping it wasn't what he thought it was.

Remembering his promise to Meiling that he would be her "fiancé" until he found someone he loved more, Syaoran calls her to tell her that he is in love with Sakura, though he is taken by surprise when Meiling arrives in Tomoeda for the day. While Meiling spends the day with her old friends, the group is attacked by a set of enchanted penguin statues at the playground.

Toya and Yukito are starring in an independent film directed by Nakuru for their school fair, and Nakuru gives Sakura a role. Sakura later begins to notice that Yukito is losing his power and is starting to fade away. Things come to a head when Yukito passes out and falls of a veranda while shooting the film, though he is saved by Toya and, secretly, Sakura. Toya finally manages to tell Yukito the truth about his power, telling off Nakuru when she attempts to interfere. In order to maintain Yue's power and existence, thus allowing Yukito to survive, Toya sacrifices his powers to save him, though losing the ability to sense when Sakura is in danger. As such, Toya has Yue promise to protect Sakura, as well as himself. Having overheard, Sakura realizes that Toya had indeed known about her secret all along. She confronts Kero about why he didn't tell her about Yue/Yukito; Kero explains that he did so to prevent her from blaming herself, since her power alone wasn’t enough to sustain him, and thus act irrationally because of it. Not wanting Yukito to disappear again, Sakura resolves to confess her true feelings to him.

After viewing Nakuru's film, Sakura tours the high school fair with her friends, while Toya comforts Yukito when he appears troubled by the fact that he is not human. Alone with Yukito in one of the attractions, Sakura tells Yukito how much she likes him. However, Yukito gently rebuffs her, saying that her love for him is merely platonic, and that he already has someone he loves; Sakura, in a rare moment of insight, realizes that person to be her brother, Toya. Yukito tells Sakura that the person she loves most is still out there when Sakura senses Clow Reed's presence once more. Using the Maze and Illusion cards, Sakura manages to trap the presence and discovers it to be coming from Eriol, though she loses consciousness. Eriol jumbles her memory of the discovery, acknowledging that she has indeed grown powerful to find him. Sakura tells Syaoran of her experience with Yukito and, despite her understanding and acceptance of the matter, begins to cry. Knowing that now is not the time to tell her that he loves her, Syaoran comforts her and assures her that she will find the person who she loves the most.

Naoko tells everyone a scary story about a bright light she chased into the woods. After school, Sakura and her friends visit the woods to see the light Naoko saw. When they do see it, everyone runs in fear, claiming they saw something appearing from the light, but everyone saw something different. Sakura returns at night in case it was a card despite her fear of ghosts. After following it near a cliff, the light takes the form of Sakura's deceased mother, Nadeshiko. Sakura, who is delighted to see her mother, walks towards it and off the cliff, but she is saved by an unknown entity and safely lowered into Yukito arms who is passing by. Sakura returns to the cliff a few days later and once again walks off the cliff. She realizes that it couldn't be her mother and discovers it to be really The Illusion.

Sakura, usually cheerful, is forlorn by Syaoran's confidence and obviously superior skill. Rika and Tomoyo take Sakura to a shop to try to cheer her up. The three each buy brooches and return to Sakura's house for tea and pudding. When Rika puts on her brooch, The Sword takes control of her and attacks Sakura with a sword. Syaoran saves Sakura who refuses to attack Rika and stops him from attacking her as well. Using Illision to distract Rika, Sakura is given the chance to capture Sword. The next day, Syaoran is dismayed when he sees Sakura offer a gift of chocolate to Yukito, and quickly gives sweets of his own. Tomoyo has to explain to Sakura that Syaoran is "interested" in Yukito just like Sakura is.

Sakura and Kero encounter some problems with time as Sakura, Kero and Syaroan find that they are the only ones who realize that Time is starting the same day over and over and over again. It's time for Sakura to take action and capture this time-meddling Clow Card!

Sakura is invited to the high school culture festival. She meets Tomoyo and Syaoran there and catches a play by Yukito and Toya's class. During the play, a mist forms outside the auditorium and enters through the vents where it destroys the stage and puts Toyo and a girl named Yoko in danger. Sakura and Syaoran head towards the lighting room where Sakura summons the Shadow card to capture the Mist card and Syaoran summons the wind to save the falling Toya and Yoko.

After waking up early, Sakura goes for a skate and remembers the dream she had the night before about a mysterious figure standing on the Tokyo tower. She soon ends up at the shrine were the Maze card was captured and meets Ms Mizuki. Sakura and Yukito go on to help Ms Mizuki clean the shrine. After school, Sakura and her father are together and it is revealed that Toya know Ms Mizuki when she was an assistant teacher while Toya was in Junior High. Kero is soon alerted to a strong presence coming from the shrine. While at the shrine they meet up with Syaoran who is also looking for the card. Kero soon slopes off to get drinks and Syaoran and Sakura are left to talk. Syaoran once again warns Sakura of how dangerous Ms Mizuki can be and they both admit their love for Yukito. Syaoran is so embarrassed that he runs off in distress and Sakura is swallowed by a dark shadow. It is soon revealed that it is the work of the Return card and that she has gone back in time. While in the past Sakura see a number of scenes involving her brother and Ms Mizuki and you find out that both appear to love each other, but she tells him to not linger in the past and look forward, since she has to go to England but, when she returns, Touya will have a new love in his life and both she and Toya will be best friends. Sakura is soon returned to the present with the help of Syaoran and the Time card and Sakura captures the Return card and it then goes to Syaoran.

Sakura’s class receives a new transfer student, Eriol Hiiragizawa, a boy from England, and he starts charming Sakura, making Syaoran jealous. Later on, Sakura receives a vision from Clow Reed that he may bring trouble to her, and that night an unnatural storm hits town. Sakura decides to investigate, and discovers that the storm was created by magic. Sakura tries to end the storm, however trouble arises when Sakura attempts to use her Clow Cards.

Sakura grows in magical strength and power for every Clow Card she transforms into a Sakura Card, while Yue's energy begins to falter. Yue also comes to the realization that Eriol is in fact Clow Reed and transforms in front of him. However, Eriol makes Yukito faint and erases his memory of him ever realizing who Eriol truly is; Clow Reed, since he is not yet ready to reveal himself and also reverses Yue's transformation back into Yukito. Syaoran, in the meantime, has fully realized his strong romantic feelings for Sakura and consults with Tomoyo, who helps him deal with his jealousy towards Eriol and gives him the confidence (just barely, though) to speak his mind to the oblivious Sakura. Before he can do so, however, both he and Sakura sense Clow Reed's presence once again, this time in the form of a basketball that leads them through the school at night.

At an art museum trip, Sakura witnesses a boy attempting to change a painting. During the commotion, she couldn't hear anything and Kero is sure that it was caused by a Clow Card, The Silent. Sakura sneaks out of the house at night and into the museum where they meet the boy from earlier also sneaking in. The boy, Yūki Tachibana, explains the painting is by his deceased father and his mission to restore the painting which a Clow Card has covered up. Every time Sakura attempts to capture the card, it transports the group outside. Using The Shadow, Sakura is able to silently capture Silent from a distance restoring the painting and discovering Yūki is actually a girl. A stranger, dressed in an odd costume, appears at the end of the episode and quietly mutters that he senses a Clow Card.

It's Sports Day at Sakura's school so family members has come to cheer the students on. Sakura meets Tomoyo's mother, Sonomi Daidōji for the first time. When Sonomi and Sakura's father, Fujitaka, meet, both are shocked. From their conversation, it is revealed that Sonomi is a cousin to Sakura's mother and she blames Fujitaka for her death, though not in any direct way. While Sonomi and Fujitaka race in the parent's race, there is a shower of flower petals. Sakura suspects a Clow Card and finds The Flower on the roof of the school.

Sakura is invited to Tomoyo's home for the first time. She is shocked to find Tomoyo's house to be an elaborate mansion with maids. Sonomi rushes over when she hears of Sakura's visit and shares the memories of Nadeshiko with Sakura over tea. While Sonomi is taking care of business over the phone, Tomoyo presents a special box and explains the key to the box bounces out whenever she tries to open it and Kero senses it's the work of a Clow Card. Sakura uses the Sword card to slice away the protective barrier of the Shield card and captures it. Inside the box is a dried bouquet of cherry blossoms from Sakura's mother's wedding and the first present Sakura ever gave Tomoyo, an eraser shaped like a bunny.

Sakura's family and Yukito takes a vacation to the country side. Sakura meets the old owner of a country mansion near their rented cottage. He invites her over for tea, tennis, and they become good friends. He shows her the room of his granddaughter, now deceased, and gives Sakura clothes that once belonged to her. The next day, Fujitaka gives Sakura cookies to give to the old man. When she brings them out to eat, the old man asks her about her father. On the last day of her vacation, Sakura asks the old man to stand in the balcony of his granddaughter's room. From a distance, Sakura uses the Rain card to give the old man a rainbow as a goodbye gift. Sonomi comes out of hiding to speak with the old man to reveal the old man is the grandfather of both Sonomi and Nadeshiko, and Sakura's great grandfather.