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.

Sakura and her class is on a trip to the beach for a few days. On the first night, Naoko tells one of her scary story causing Sakura to flee to the teacher's lodging, but she is found by Syaoran who senses something in a cave nearby. Together at the beach, the two have their first civil conversation where Syaoran tells Sakura about Wei, a person he lives with. A test of courage is held the next night where the students must enter the cave and place a candle next to the shrine inside. But once inside, Sakura's friends begin to disappear. Syaoran, the only one left, forbids Sakura from panicking and walks her through the process of capturing the Erase card even while he's starting to fade away. Syaoran refuses the card after Sakura offers to give it to him.

Sakura visits a festival with Tomoyo, Yukito, and Toya. After meeting Chiharu and Takashi, Sakura and Yukito wander away from the group where they find glowing lights falling from a tree like snow at the back of the shine — just like a dream Sakura envisioned the night before. Just as Sakura is about tell Yukito something, she is interrupted by their friends. When everyone leaves for snow cones, Sakura captures The Glow.

The summer holidays are coming to an end and Sakura still has a lot of summer vacation homework to do. Making a deal with her brother and Kero to help her, Sakura is left with only a book report and meets with Tomoyo at the library. There, they meet Syaoran who refuses to share a library cubicle with them because his fortune predicted bad luck with women. The book Sakura needs for her book report is missing so Sakura and Tomoyo search the library, but notice the book disappearing and reappearing in different places. The book eventually appears outside the library where they meet Syaoran who is also after the book. Kero reveals it’s the work of the Move card and for the first time, thanks to Move's unpredictable actions, Sakura is forced to rely solely upon her magical senses to catch a card. Sakura is rewarded with the book and a new card, but accidentally plunges into the river, taking Syaoran with her. Syaoran invites the girls over to his place so Sakura can change into dry clothes, but to everybody’s surprise, a Chinese girl enters the apartment and leaps on Syaoran with a hug.

When Syaoran enters the room, he's markedly pale and haggard compared to his usual tough-and-healthy look. When Meiling enters the room, it's clear that her presence has exhausted him and he is desperate to escape it. Mr. Terada explains that she is from Hong Kong and cousin to Syaoran. Meiling is quick to add that she is actually his fiancee, and obviously believes Sakura wants to take Syaoran away from her. Syaoran asks Meiling why she came, and she answers that she was lonely for him. He explains that he's not going back until he gets the Clow Cards, but she doesn't particularly care about that. She reminds him that a fortune-teller in Hong Kong predicted someone else would get them, a reminder that clearly grates on his nerves. It's only after he makes it clear he won't return home without the Cards that Meiling decides she will get involved and 'help', so that he can collect them faster.

During a school race, Meiling is determined to win with Syaoran, in their usual "One-Two Finish" they were known for in their previous school. During the race, both Syaoran and Sakura take off at top speed after seeing that Yukito is watching. As the run, the Loop card causes traps Sakura and Syaoran, causing them to run in circles. After they realize what has happened, Sakura is able to use the Sword card to cut the loop. Syaoran carries Meiling, who hurt her ankle, the rest of the way to the finish line, joined by Sakura.

Sakura's father has an important presentation to complete so Sakura and her brother decide to help by taking on all the chores around the house. Sakura decides to do more and brings a snack for her father at the university. While she is there, the Sleep card shows up and starts to make all the students and professors fall asleep. Sakura manages to capture the card with the help of Windy, however her father's laptop is ruined in the process. Although her father forgives her, Sakura still feels guilty so her father deicides to make her his personal assistant and they eventually get the presentation finished.

When a rumor starts that a voice is heard in the elementary school music classroom, everyone assumes that it is a ghost singing (much to Sakura's dismay). That evening, Toya comes home with Yukito for a sleepover, much to Sakura's liking. When they arrive home Sakura asks Yukito for tea, and Toya asks, too. When they sit down and talk about the ghost, much to Sakura's dismay yet again, Toya starts on about some of the students hearing the voice some time at ten o'clock in the night. Sakura gets frightened, but then Yukito adds that he heard that the voice was really wonderful, so Sakura decides that she will check it out in case of a Clow Card and to record it. When they get there Sakura is obviously frightened. Then she gets a surprise from Syaoran and Meilin. Suddenly, they hear a voice coming from the music room. They decide to check it out. When they arrive at the music room. Meilin suddenly leaps up and opens the door to the room making the Clow Card disappear. Although Sakura recognizes the song and remembers that it is the song Tomoyo sang to her and will be doing the song for the chorus. They hear it yet again and follow it to the stairs. During the chase, Syaoran and Kero tell the rest that the Clow Card is the Song card.

When Tomoyo comes over to measure Sakura for a new outfit, Sakura comes in contact with the Little card, which shrinks her and her magic. While Tomoyo and Kero search for her, Sakura winds up in the backyard, being chased by a cat and a praying mantis. When Toya and Yukito come home, Tomoyo hides Kero while Sakura confronts the Little card, but it runs away from her. Eventually, Sakura chases the card into the kitchen, where it almost shrinks Toya, but it bounces away. The card bounces up the stairs, and Sakura gives up because it was not possible to continue. Luckily, she was then found by Kero, who explained the Little card to her. Meanwhile, Tomoyo is in Sakura's room when she hears the Little card. She is about to touch it when Sakura comes riding on Kero and runs into the Little card, thus returning to her normal size. She then seals the Little card. Later, Sakura, Tomoyo, Toya, and Yukito are enjoying Tomoyo's strawberry tart that she brought, when Sakura remembers that she promised Kero a piece. In the end, Sakura manages to get him a tiny slice. He whines and then uses the Little card to make himself tiny and eat the now huge slice of cake.

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.

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.

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.

One of Sakura's friends makes a jump and passes a P.E. test. But she and her other friends all think it was because she made a wish on the "Jump" card. Sakura becomes worried and asks to see she is relieved to see that it is not the real Jump card, and she still asks where they got them. They tell them at Twin Bells. Both her and Tomoyo go to check it out. They see Maelin there. After seeing that one card is missing they ask who bought it and what it was. when they discover that it is a real Clow card they go looking for whoever bought it. After running into Syaoran, he and Sakura find Meiling. She refuses at first to give the card back, but when she releases the Shot card's power accidentally and Syaoran is hurt, Sakura comes up with a plan to capture it and does so.

Sakura practices in the kitchen with her father for an upcoming home-economics class, as Sakura is worried about how she will do. Sakura's classmates decide which cakes they will bake. The following day, everyone begins making their various cakes, but after leaving them to bake over lunch, they come back to find them to be far too sweet. The next day, everyone starts over and make sure they measure the ingredients correctly. Sakura and Syaoran sense a Clow Card, and afterwards everyone except them exits the classroom. They discover it to be the Sweet card, which flies around the room turning everything into sweets and confections. Sakura captures the card after throwing salt on it to temporarily immobilize it, which causes the room to revert back to normal. After everyone comes back, and the cakes have turned out great, except for Meilin's, who made hers too hard.

When an attempt at capturing the Dash card doesn't go so well, Sakura's upperclassman Rei, a girl from the track club, finds it and takes it home. After the Dash enchants Rei to become faster as thanks for her kindness, Sakura has a hard time capturing because she feels bad, but Syaoran doesn't and one day he finds and lures it to the woods. After Kero and Syaoran tell her that it'd be worse if Rei won her races through "cheating", Sakura then captures it. But it goes to Syaoran, since he weakened it. During an upcoming tournament, Rei is sad upon the loss of her friend, but Syaoran casts an illusion of the Dash card at the race fields; encouraged, Rei wins without the power of magic.

Naoko, Sakura's classmate and friend, goes to a bookstore and buys a mysterious book which has no title and the things she writes in it comes to life. Sakura catches the card which appears to be the Create card by using the newly captured Big to enlarge her size and seal the dragon she encountered away.

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.

Sakura’s fourth grade class takes a trip to the town’s ice skating rink. At the ice skating rink, the students begin to feel low, freezing temperatures due to the Freeze card. Eventually, the Freeze card beings to freeze everyone by covering them with ice, except those with magical powers, which include Sakura, Syaoran, and Ms. McKenzie, who was hiding near the back of the rink during Freeze’s appearance. With the help of Syaoran’s distractions, Sakura is able to capture the Freeze card into a clow card and ultimately, Syaoran became the master of the Freeze card due to his idea of getting Freeze to appear out of the ice rink.

Sakura and Yukito participate as a two people team in the quiz tournament. As they get to the 10th question which is the last, Ms. Mizuki warns them about the full moon tonight. They go in the forest and then suddenly Sakura becomes dazed and begins to fall off the cliff. Yukito dashes to Sakura and covers her while his leg becomes injured.

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.