Sakura Kinomoto awakens from a dream of standing near the Tokyo Tower. She introduces herself, her family, and her friends. After coming home from a normal day at school, Sakura hears a sound coming from the basement. She finds a glowing book and opens it to find a deck of 52 cards. When she accidentally activates the Windy card, the other cards blow out of her house. Cerberus appears from the book and formally appoints Sakura as the "Cardcaptor" and gives her the Sealing Wand. Sakura captures the Fly Card, but she adamantly insists she does not want the job. All the same, she shows quick thinking, considerable magical power, and sheer joy on her first ride on the tamed Fly

Tomoyo meets Cerberus after she discovers Sakura's secret and gets a full explanation of the lost Clow Cards and Sakura's designation as Cardcaptor. Cerberus gets given the nickname "Kero-chan" that will stick for the rest of the series. The next day, the students find the school's desks and equipment in large piles. Kero believes it was the work of the card and forces Sakura to go to school at night where she confronts The Shadow. Using the Windy card's binding ability, Sakura is able to capture the Shadow card. Sakura finally accepts her role as a Cardcaptor because of Tomoyo's support.

Sakura's class is on a field trip to the aquarium. During the penguin show, something catches the trainer's leg and a penguin and pulls them into the water, but they are saved by Sakura's brother, Toya, who is working part-time there. At school, Tomoyo gives Sakura and Cerberus mobile phones and on the way home, Sakura bumps into Yukito who invites her on a casual "date" which is at a cafe where Yukito knew Toya was working. While they are eating, The Watery breaks the glass of the aquarium causing a flood. For the first time Sakura has to formulate a plan to capture a card, rather than jumping into battle and attacking with Windy. Using her wits and an unintentional clue from Yukito, she lures Watery into a freezer to immobilizes and capture it.

While cleaning the house, Sakura finds two dormant Clow Cards, The Wood and The Rain. But while running an errand for her father, the two cards activate creating a jungle inside the house. Sakura uses The Watery to capture The Rain card and The Wood yields on her own. Sakura gets the hard-earned lesson that a card is not fully subdued until she signs her name on it.

On the way to school, Sakura meets Maki Matsumoto who is opening a stuffed doll shop called Twin Bells. Sakura and her friends visit the shop after school to find most of the merchandise unpacked, so they offer to help. Chiharu Mihara, who has a fondness for stuffed animals, buys a stuffed panda, but it disappears shortly after taking it home. Sakura discovers the panda back in Twin Bells and Maki explain the reason for opening the shop and her business has been plagued by mysterious happenings that almost forced her to close down. While Tomoyo distracts Maki in the back, Sakura and Kero search the shop to find The Jump, which escapes with all the stuffed dolls in the shop. At Penguin Park, The Jump grows into a giant by absorbing the stuffed dolls, but it knocks itself out after it trips and falls allowing Sakura to capture it.

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.

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.

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.

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.

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.

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.

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’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.

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.

Exhausted from the events of the other night, Sakura remains in bed and sleeps into the afternoon before being visited by Syaoran and Tomoyo. Kero explains that Sakura used a great deal of power to transform the Clow Card, explaining her sudden tiredness. Since the Fiery Card was transformed to be under jurisdiction of Sakura's power, Sakura's friends henceforth transform the cards into "Sakura Cards". Later at school, Sakura overhears Eriol playing the piano and has Tomoyo sing to his music; unbeknownst to them, however, Eriol enchants the piano while he plays.

Sakura begins to wonder if the bizarre goings on are connected to Clow Reed's presence, though she is aware that Clow is long deceased. At recess, Rika shows everyone a teddy bear she made. Sakura decides to get her own teddy-bear-making kit at the craft store where she sees Eriol buying several spools of string. That night, Sakura and Kero once again sense Clow Reed's presence and meet up with Syaoran and Tomoyo.

Several people at school have started making their own teddy bears to give to their loved ones, while Eriol helps Sakura make her bear for Yukito, secretly enchanting one of its ears. Syaoran, who also has feelings for Yukito and has made his own bear, begins falling in love with Sakura as well. Yue approaches the confused Syaoran and tells him that the reason he seems to be in love with Yukito is that he, having descended from Clow Reed, feels an attraction to the moon powers Yue emits as a creation of Clow. That night, Sakura gives Yukito the bear, only to see it grow in size in response to Eriol's magic.

Yue secretly confides with Kerberos that he has recently been losing his energy, and that Sakura's powers alone aren't enough to help him maintain himself; he adds that if his power disappears, both he and his alter ego Yukito, who is oblivious to this incident but growing increasingly aware of it, will fade from existence. Toya, who is aware of Yukito's predicament, attempts to tell him the truth, but is once again interrupted by Nakuru, making it clear she is doing so on purpose. Meanwhile, Sakura's attention is drawn to a large, deep hole in the middle of the playground. She is able to enter the hole, though her friends are not since it is sealed by Clow Reed's magic.

Sakura learns that the Clow Cards she is unable to use are beginning to lose their power, and will become ordinary cards if they aren't converted into Sakura Cards. Unwilling to let this happen, Sakura brings her Star Wand and despite Kero's misgivings, recklessly converts several cards at once although she's left weakened. However, she loses control of one of the cards, the Dash, which panics and flees, possessing Toya's bike which Eriol had enchanted earlier while helping Sakura clean her yard.

Fujitaka gives Sakura her mother's old calendar, and learns about her great-grandfather (the two had previously met, though Sakura remains unaware of his identity) and how he disapproved of his granddaughter's marriage to Fujitaka. Hoping to set things right, Sakura hand-makes a gift and uses the Flower card to decorate it, along with a letter about how happy her mother was.

While reading Alice in Wonderland, Sakura is sucked into the book's fantasy due to another of Eriol's enchantments, this time on a leaf he gave Sakura to use as a bookmark. There she meets the story's characters who have taken on the forms of her friends and family: Eriol is the Cheshire Cat, Yukito is the White Rabbit, Toya is the Mad Hatter, Syaoran is Tweedle-Dum and Tweedle-Dee, Tomoyo is Humpty Dumpty, and Kero is the Red Queen.

Sakura's school is hosting a bazaar, and Kero attends to eat sweets, hiding in the woods. Nakuru, meanwhile, brings Spinel Sun along and hides him in the same forest while she attends the bazaar. Kero meets Suppie (the pet name Nakuru gave him) but is completely oblivious to his true nature and befriends him, forcing him to eat some of the sweets. As a result, Suppie becomes intoxicated by the sugar and goes on an eating binge throughout the school. Kero, who is unable to explain the predicament to Sakura, asks her to use the Sleep card on all the customers, allowing him to get rid of Suppie.

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.

It's the new term, and the hot topic at school is clubs! Sakura and Tomoyo decide to join the same clubs they did in elementary school, cheerleading and chorus.

It's been raining buckets all day. Sakura and Tomoyo take shelter in a park on the way home from school, and suddenly the Key of Dreams at Sakura's chest begins to shine... Is it the work of a card?

A new transfer student named Akiho Shinomoto joins Sakura's class. She's just arrived in Japan after living overseas, so her Japanese is still very stiff and formal. Sakura invites her to eat lunch with her group, excited to make a new friend.

Sakura is having a flower-viewing party with her friends Tomoyo, Syaoran, Chiharu, Naoko, and Yamazaki, as well as the new transfer student Akiho.

Sakura continues to face the hooded figure in her dreams. At school, everyone says they want to hear Akiho sing again after being charmed by her voice at their flower-viewing party, so they meet in the music room after classes are over.

Sakura and Kero-chan visit Tomoyo's house to test the abilities of the Record card. Tomoyo's mother appears and gives Sakura an enthusiastic welcome, then the girls head outside to test the card.

Sakura finds out that Akiho has moved into the mansion formerly inhabited by Clow Reed's reincarnation, Eriol. She pays a visit with Tomoyo and meets Kaito, the butler who's been taking care of Akiho since her childhood.

Sakura invites Syaoran out for the day with tickets given to her by her father. She's worked hard on the rolled omelets for their lunch, and now they make their way to the aquarium Sakura visited when she captured the Clow Card, Watery.

Akiho pays a visit to Sakura's house one evening while her father and brother are both away. They look at Sakura's elementary school pictures and have dinner together, but then Akiho suddenly falls asleep.