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.

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 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.

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!

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 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

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.

When Sakura senses a card late at night, she heads to Tsukimine Shrine with Kero-chan, Tomoyo, and Syaoran.

Cerberus and Yue meet with Eriol via magic to discuss Sakura's new cards. Eriol has found out that Kaito took something from the magic association he once belonged to, but at that moment, Kaito's magic severs the trio's communication link.

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.

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 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's class is visiting the zoo for a field trip and her group is assigned to observe the elephants. Near noon, something begins to break open the cages causing chaos among the visitors and Kero is positive it's a Clow Card. The Power card, although invisible, begins to torment the elephants and Sakura steps in to save them by challenging it to a game of tug-of-war. Sakura is no match for the Power card even with the help of the elephants. Just as Sakura is about to lose, Syaoran uses the Time card to stop time to help her win the battle, thus tricking Power into surrendering.

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.

Syaoran captures his second Clow Card after defeating the Storm card. Tension develops between Kero and Sakura over the Syaoran issue which builds into a fight the next day after Kero makes a mess after building a room inside Sakura's desk drawer. While Sakura is at school, Kero eats liquor-filled chocolate and wanders out the window drunk. The next day, he finds himself with a young girl named Akane who lives alone with her mother. Unable to escape, Kero secretly contacts the worried Sakura by fax. Akane wishes she could fly to see her father in heaven and the Float card makes her dreams come true. Sakura comes to her rescue and brings Kero back home. As a way of making amends, Sakura redesigns her bottom desk drawer to become Cerberus's bedroom from now on.

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.