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's grade goes on a field trip to pick strawberries. Sakura and Tomoyo bump into Yukito and Toya who are working part-time at the strawberry field. On the way to the greenhouse, Syaoran senses something from the storehouse, but Meilin pushes him along. The class enters the greenhouse and begins picking strawberries. Sakura hears the door to the storehouse will not open, but when she and Tomoyo go to investigate, they find it open. Syaoran and Meilin come into the storehouse, and Syaoran says that he feels a strange presence. The door suddenly closes and locks them inside. Syaoran informs the group that it it the Lock card that has trapped them. After Rika, Naoko, and Chiharu come to the storehouse, they go look for Ms. Mizuki and tell Toya and Yukito. While looking for a key to unlock the door, Sakura sees Ms. Mizuki through the window, who gives her a hint, but Ms. Mizuki then disappears. Sakura realizes that Ms. Mizuki was trying to tell her to use her key. The Lock card shows its true form when Sakura tries to put her key into the lock. Syaoran seals the exits and Sakura quickly seals the Lock card before it can get into the keyhole. Toya, Yukito, Rika, and Naoko come into the messy storehouse, now that the Lock card has been captured. Sakura and the others clean up the storehouse together. Sakura's group learns how to make and bakes desserts with strawberries. After the desserts are made, Sakura brings a piece to Toya and Yukito.

Sakura has a fever, but goes to school anyway because of a group project. Later, Sakura gets dizzy and is sent home with Toya by the nurse. Toya stays home to watch over her. When Toya is making food for her, Sakura senses a Clow Card, and it turns out to be the Cloud card. Sakura uses the Mirror card to make a clone of herself, so Toya will not notice that she is gone. Sakura, using the Fly card so she can capture the Cloud card. Toya comes in Sakura's room with food and offers it to Sakura's clone. Sakura travels toward the Cloud card, but when she is blown off her staff, Syaoran saves her with a wind spell. Sakura learns that Syaoran and Meilin are going after the Cloud card as well. Back in Sakura's room, Sakura's clone asks for the medicine and Toya replies that she should not take medicine when she is not sick, because she is not Sakura. Toya asks the Mirror card to hide the fact that he has a vague idea of what Sakura is doing and the Mirror card agrees. Back outside, Syaoran hits the Cloud card with various spells and gets it to its original form and Sakura seals it. The card is Syaoran's, but he gives it to Sakura. Sakura returns to her room and falls asleep in her bed. Nadeshiko appears and heals Sakura. She tells Toya that she was a bit worried and then tells Sakura to do her best, before disappearing. Sakura's father appears saying that he was worried about Sakura because she was acting strange this morning, and Toya tells him his hunch was right and that mother appeared. The next morning, Sakura is as cheerful as ever, and her father is home helping make breakfast. Sakura thanks her mother for staying by her side.

Sakura, Tomoyo, Meilin and Syaoran head into town for a day of fun. The four are not alone in their venture as the Dream, in the form of a butterfly, tags along. When the group enters Tokyo Tower to see an exhibit there, Sakura falls under the Dream's spell. At first, the vision that the Dream presents to Sakura is comical. Later, the Dream takes a more serious tone by expanding upon Sakura's reoccurring dreams concerning the Clow guardians' Final Judgment. Sakura becomes frightened of the images of this future, however, the Dream flashes clips from Sakura's past to remind Sakura of all the obstacles that she has overcome. Outside of Sakura's dream, Syaoran realizes that something is wrong and uses the Time card to freeze the Dream card. Snapped out of the Dream's spell, Sakura is able to successfully capture the Dream card. However, as it was Syaoran that stopped the card's effects, the Dream card belongs to Syaoran.

Ms. Mizuki announces that the class will by doing a play for the school arts festival. Sakura realizes that the woman she sees in her reoccurring dream is Ms. Mizuki. Roles are assigned by amida drawing. Sakura has the role of the prince and Syaoran is the princess. The two have lunch with Yukito, who asks about the play. Sakura and Syaoran are too embarrassed to tell him what roles they are playing. They agree to practice their lines together in the morning at school. Toya makes Sakura breakfast and warns her about doing "reckless" things. Sakura meets Syaoran in a hallway and the Sand card rushes around behind them. They practice outside and almost get to the kissing scene, when the Sand card forms a vortex around them. They get away using Fly, but Syaoran gets caught in the vortex again. Sakura uses Watery and Syaoran uses Freeze to freeze the Sand. Sakura seals the card and it comes to both of them, but she lets Syaoran have it.

Sakura and Syaoran are working hard at memorizing the play. Finally the day of the play comes, and after a few denials about going out on stage from Syaoran, the play is on. The play goes well until right before Sakura and Syaoran kiss, when the Dark card appears. Sakura is almost lost in the Dark card until she realizes that she holds the Light card in her heart. The two card counteract each other and show themselves. Sakura seals both cards and before being sealed, they tell her that the final judgment is coming and that is will be up to Yue.

Meilin gets a call from her mother, who wants her to come home. Meilin tells Sakura the next day that she is going back to Hong Kong next week. Syaoran appears, and asks Meilin if she told the teacher she is going back to Hong Kong yet. Meilin asks Syaoran if he feels she is getting in his way, and Syaoran says that is not it. Meilin runs off, calling Syaoran an idiot. At the end of school, Sakura invites Meilin to her house and they have a chat with tea and sweets. Sakura tries to make Meilin feel that she is not a nuisance to Syaoran. Meilin tells Sakura about how she fell in love with Syaoran. In the middle of their conversation, Sakura senses a Clow Card. Meilin decides not to go, but Sakura drags her along and tells her there are things only she can do. Meanwhile, Syaoran is getting beaten by the Twin card. After a couple of failed attempts, Sakura thinks that Meilin and Syaoran can work together to keep the two bodies of the Twin card immobilized, so she can seal them away; they try it, and it works. Sakura seals the Twin card, and it goes to Syaoran because he and Meilin weakened it. Syaoran tells Meilin that he never thought that she was in his way. Sakura, Tomoyo, and Kero go to the airport with Syaoran to say goodbye to Wei and Meilin. Meilin asks Syaoran if he remembers the promise, which is until Syaoran finds a girl he likes more than her, she will be his bride. Meilin whispers a thank you to Sakura for saving them with her magic, before she leaves.

Sakura once again has the dream in which she is facing the Tokyo Tower. She clearly sees Ms. Mizuki, but this time, Mizuki is accompanied by another figure with long hair and wings. She wakes up early to see Yukito compete in an archery competition. Sakura explains what she knows of her dream to Kero before running down to make breakfast. She meets up with Syaoran and Tomoyo at the archery competition, and Kero tags along too. At the archery tournament, Sakura finds that Ms. Mizuki is one of the challengers and ends up in the finals alongside Yukito. During the fierce match, Kero pokes his head out of Sakura's bag upon sensing tremendous magical power, shooting a piercing glare at Ms. Mizuki. Sensing his gaze, Ms. Mizuki loses her focus and the tournament. Later during lunch, Sakura discovers that Kero is missing from her bag. Searching for him, she is astonished to find him in the middle of a private conversation with Ms. Mizuki. While walking home, they run into Toya once again, this time dressed in a bear costume giving out balloons. After he leaves, there is an earthquake, likely caused by the final Clow Card.

The earthquake was caused by the Earthy card. Ms. Mizuki is nearby, but there is nothing going on around her. Sakura uses to Sleep card to put everyone except herself, Kero, Tomoyo, and Syaoran asleep; Ms. Mizuki is not affected by the card, however. Sakura uses the Fly card to see from above; while Syaoran makes sure everyone is safe. Sakura eventually uses the Woody card to seal it away. Now with the final card in her possession, Kero is able to transform into his true form. After a short celebration, Syaoran explains that Kerberos, representing the sun, is one of two guardians of the Clow Cards, the other being Yue the judge, representing the moon. Kero explains that the sole owner of the cards will be determined after Yue appears. Suddenly, Yukito magically floats with a light blue aura, and turns into Yue. Ms. Mizuki explains to Sakura that Yukito is Yue. Yue begins the Final Judgment of Syaoran, who tries to fight Yue with a seal, but Yue tells him that it is useless, and he can only use the Clow Cards he currently has. Syaoran tries to use the Time card, but since it is under Yue's jurisdiction, Yue can use it against him. Syaoran is defeated, and it is time for Sakura's Final Judgment.

Sakura initially refuses to fight Yue, but after he repeatedly attacks her she tries to find card that can confine him without hurting him. She uses the Woody card, but it is a card under Yue's sign of the moon, and he turns it against her, and Yue declares she has failed. Sakura learns that if she fails the Final Judgment, everyone who has ever had anything to do with the cards will forget their feelings for the person they love the most. After seeing a vision of such a world, Ms. Mizuki uses the bell to enable her to break free from Woody's hold. She explains that her bell was created by Clow Reed to give Sakura another chance. Ready to try again, Sakura releases her wand and it transforms, the end changing to a Star. She call's Windy, which Yue denounces as being under him as well, but this time he is unable to turn it against her and is captured. Sakura expresses her understanding of his love for Clow, promises to try her best, asking if they can be friends rather than her being his master. Yue declares the trial successful and acknowledges her as his and Kero's new master. Sakura has a vision of Clow Reed who thanks her and explains that her power is of the Stars, rather than the Sun or Moon. Sakura celebrates with Tomoyo and Syaoran, while Kero and Yue chat briefly before they return to their false forms.