Sakura has the dream of Tokyo Tower and Clow Cards again, in which she faintly recognizes the one standing on the tower in the shadow could be Ms. Mizuki. Then she is woken up by Kero. It is the first day of her new school year, when Sakura has become a fifth grader.
On the way to school, Sakura finds her good luck, that Yukito gives her a gift for her promotion and for her birthday. Furthermore, she is surprised and delighted that her new homeroom teacher turns out to be Ms. Mizuki. When the teacher says something mysterious, it begins to snow despite the time of spring.
It is still snowing when Sakura gets back home. She unwraps the gift from Yukito, the inside is a lovely wristwatch. She wears the watch with joy. When she is cooking dinner, Touya come home soaked with snow. Surprisingly, the snow is about three feet deep outside. It is the work of the Snow Card.
Sakura, Tomoyo, and Kero come to Penguin Park for a card capture, then they see Syaoran and Meiling come. All of a sudden, a blizzard occurs, and it follows Sakura and Syaoran everywhere they run. The blizzard seems like attacking the ones with magical powers. Sakura and Syaoran take on the Fly and rise up in the night sky. No matter how fast they fly, the swirling blizzard is trying to swallow them. Sakura finds her wristwatch gone in the escape, so she gets mad, stands on the archway of Tsukimine Shrine, and releases the Firey Card. The Firey thaws all the snow in town, and helps Sakura seal the Snow Card. Afterwards, when Sakura is crying over her wristwatch, Ms. Mizuki shows up and gives her watch back. Mysteriously, the teacher walks back into the shrine.
Sakura and her friends are enjoying a picnic under the cherry tree full of blossoms. When Tomoyo is singing a karaoke, a mysterious glow floats in the tree stealthly.
These days, Tomoyo has been practicing her set piece, as she is to take a solo in her next chorus competition. Sakura, during her cheerleading practice, hears Tomoyo singing, and she walks closer to the music classroom to have a better listen, when she senses a Clow Card. Despite her attention, the Card rushes into the classroom and steals Tomoyo's pure voice. Immediately, her bodyguards pick her up to take her to the doctor. Later, Kero comments that it was the work of the Voice Card, which has stolen its favorite voice. Tomoyo's mother Sonomi in anxiety decides to spend the next day with her daughter, taking her day off though she is the CEO. Tomoyo bravely wtites down to Sonomi not to worry, so she gave her daughter a hug and tells her not to push herself too hard.
Next day, Sakura and Syaoran comes to Tomoyo's house. Since Tomoyo smiles at them that she is all right, Sakura feels it bitter that she blames herself that the accident was her own fault. Not an idea did they think of, no matter how hard, and no matter how long they tried. Nevertheless, Tomoyo does not show her weakness, so conversely Sakura breaks into tears. At this time, Syaoran comes up with the idea to have the Song Card sing in Tomoyo's voice. Just as he expected, the Voice Card appears as she hears the voice she has already stolen. Syaoran spiritually encloses the room with his incantation cards, and Sakura captured the Voice Card. Getting freed from the Card's mischief, Tomoyo gets her voice back.
In the chorus competition, the classmates enjoy listening to Tomoyo singing her solo in her crystal voice. She is singing the song with a caring heart toward Sakura.
Sakura's class come to this strawberry plantation for their field trip, where Sakura bumps into Yukito and Touya working in the plantation because their school is out. The field trip is scheduled that they gather strawberries in the morning, and they bake some cake with their harvest in the afternoon.
Sakura has touble gathering strawberries because she wants to take as good strawberries as possible and she can not tell which ones are good. Yukito comes up to her and tells how to chose good ones, so she is fascinated by this sweet time. Getting jealousely, Syaoran gives his harvest to Yukito without a word.
Unfortunately, they hear a bad news during the luch time, that the cookery planned in the afternoon is canceled because the sorehouse where the cookery is to take place is tighly locked up. Feeling a shock, Sakura, Tomoyo, Syaoran, and Meiling runs to the sorehouse, but the door easily opens. Mysteriously, when the kids walk into the storehouse, the slums shut enclosing them. Syaoran says it is the work of the Lock Card. Being a special card, the Lock Card can not be defeated by attack cards. Tomoyo suggests that there may be the key to unclock the magic, and the kids look for the key every inch in the storehouse. In the search, Sakura slips and nearly falls off the lintel, but hanging off the lintel, she can see Ms. Mizuki pointing to the chest out the window. Sakura guesses the teacher was telling her to use the key to the seal, and she try to put it in the keyhole. Concequently, the Lock Card show its visible form and acts violently, then Syaoran block the keyhole with his incantation card, and Sakura sealed the Card before it can stick in the keyhole.
Thanks to the capture, Sakura's class enjoy the cookery in the storehouse just as scheduled. Sakura gives the cake she baked to Yukito, who is pleased with the taste. Everything seems to end up good, except that Kero gets mad at Sakura who brought him none of her cake.
In a rainny morning, Sakura wakes up and feels all fuzzy in fever. She tells Touya not to speak of her fever to Fujitaka, because he is happy to get a chance for excavation he has been waiting for. To make the matter worse, Sakura pushes herself hard to go to school, because she has to finish the poster with her group.
Sakura feels all dizzy in math class. Ms. Mizuki finds out Sakura is sick, and has Tomoyo take her to the infirmary. The school physician tells her to go home, and Meilin, Tomoyo, and Syaoran promise her to finish their poster even though she stays home sick. Meanwhile, Ms. Mizuki spiritually summons Touya to ask him to take Sakura home, then he takes her home on his back in rain.
Setting Sakura in bed and checking her temperature, he goes down to the kictchen to cook her something to eat before taking medicine. Meanwhile, creepy layers of clouds are swirling over Tomoeda, when she senses the mystical presence and gets out of bed. Although it is the work of the Cloud Card, Kero tries to stop her from going for a capture, and warns her that, if she went out, she could get even worse and Touya gets suspicious. Recklessly, she has the Mirror Card take the place of her, and leaves her house on the Fly. She finds Syaoran and Meiling already in action.
On the other hand, Touya comes into Sakura's room with pottage, and the Mirror Card sits up to eat it. However, Touya, knowing the girl in bed is not Sakura, tells the Mirror Card not to tell Sakura that he already know of her spiritual activities. Meanwhile, back at the scene of capture, Syaoran slashes through the cloud with his blade. When he sets the clouds on fire with his incantation, the Card shows its visible form, then Sakura seals it. The sealed Card floats to Syaoran, but he gives it to Sakura.
Back at home Sakura gets much worse, panting in bed from fever. As Touya is about to calling a doctor, he sees their deceased mother Nadeshiko come down. She gently pats Sakura on the forehead, her temperature immediately gets lowered, Sakura falls asleep in peace. After Nadeshiko returns up in the heaven, Fujitaka rushes back home as he somehow knows that Sakura was sick.
Next morning, Sakura come down to the dining room for breakfast, getting quite better. She says “thank you” to the picture of Nadeshiko, as she somehow knows her mother was bedide her the night before.