The clock tower bell in Sakura's school tolls at midnight, when it is not supposed to do. That sound wakes Sakura and Kero up. They have no clue what happens to the clock tower.
Next morning, Sakura has a music test, but she blows it hitting a wrong note when she is playing the recorder. When Sakura and Tomoyo are talking in the playground, Syaoran practices the recorder walking, then a soccer ball comes fly to him. With a reflex, he jumps and kicks the ball, and makes a perfect goal. That evening, Fujitaka advised Sakura to go over the practice not to make the same mistake, so she practices playing the recorder until she plays it perfectly.
What happens next day feels to Sakura something strange. She has to take the same music test, in which she makes it perfect, but nobody knows that they repeat the same day, except Syaoran who also knows about the repeation. He says that it is the work of the Clow Card that is in the clock tower. Later on that night, Sakura Tomoyo, and Kero come to school to capture the Card. When approaching the clock tower on the Fly, Sakura gets to know how to sence a Clow Card. According to Kero's comment, the Time Card merges the clock tower to make itself stronger. Sensing the approaching enemies, the Time winds back a day with its magic.
Sakura retries the next night. This time, Syaoran comes and suggests they have to sneak into the clock tower. Time Card tries to escape, but gets trapped as Syaoran set his incantation cards in advance. When Sakura seals it, the Time Card flies to Syaoran.
The incident is issued that the King Penguin Slide was upended with a threatening power. That day, Sakura goes to a zoo for her field trip. Sakura's group is assigned to the observation of elephants, and Syaoran's group to the sloths.
In her observation, Sakura finds out Kero hiding in her backpack. Sakura hears some breaking sound like an explosion, and a penguin runs across before her. On the way to the scene, she sees zebras escape from the cage, and finally arrives to the mother and baby elephants terrified by the repeating crash and thud on the ground around them. The unseen threat lifts up the mother elephant and hurl her up in the air, and Sakura has the Windy catch her safe. That is the Power Card, that turns out to be the penguin tripper in Penguin Park. When Sakura provokes it just as Kero told her, the Power follows her violently. She has to name the challenge to compete agist the Power Card, so she shouts tag-o-war.
Power is so powerful that Sakura is eailly dragged forward. Though Kero tells her to use Windy, she is too busy to do that, when the mother elephant gives her a hand with the rope. Meanwhile, Syaoran stands on a branch up in the tall tree, gazing at the competition. He freezes the moment with the Time Card, pulls the rope off Power's hand, and unfreezes the time. Both Sakura and Power yanked themselves backward, which looks as if Sakura won, then Sakura successfully seals it. Finally, Sakura uses the captured Card to place the King Penguin Slide back on its feet, later.
Yukito gave Sakura tickets to the festival of Seijou high, so she comes to the festival with Tomoyo. They make a stop at the Japanese tea room Yukito's class is running, where they see Syaoran who has already stayed there long. Afterward, Yukito shows them around the school; he challenges the basket ball team on the way, and won stuffed animals to each Sakura, Tomoyo, and Syaoran.
They see a play performed by Touya's class, which is Cinderella. Sakura gets open-mouthed when she sees Touya play Cinderella, but the girls in the school cheer with joy. Strangely, Yukito performs the sacred canned mackerel that casts a spell on Cinderella into a fair lady. That is a weird play, in which Cinderella's spiteful siters and mother are all guys, and the prince is the girl named Youko. Meanwhile, a mysterious mist seep into the theater, which corrodes and breaks the balcony when Touya and Youko are top of it. She slips off the balcony, Touya barely catches the hand of Youko hanging off. That turns out to be the work of the Mist Card, then Sakura has the Shadow wrap the Mist inside and captured it. Touya and Youko fall off at the same time, but Syaoran uses his wind magic to save them.
After the play, Youko confesses her love to Touya, but he declines meaning he loves somebody else. Nevertheless, he does a favor and dance with her, because she wanted him to.
One night, Syaoran dives into the stormy swirl, and uses his magic to disable the Stom Card, then he wins the Card. When Sakura comes home, Kero is absorbed so deeply in thought that he can't notice when Sakura talks to him. Then she gets mad and yells at him, so they start fighting.
When Sakura talks to Kero forgiving everything next morning, Kero shows her his private room he made in Sakura's desk drawer throwing every stuff inside. So they resume their fight. Angry Kero, when she is out at school, eats whiskey chololate and gets dunk, then he flies out the house. Sakura feeling a little regretful waits for him to return home, but he never returns that night.
Kero was picked up by little Akane, who convinces herself that Kero is a kitten, so she takes care of him. She lives with her mother, but she is home alone when her mother is at work, even though she is very little. Kero sends a fax to Sakura, from which Tomoyo can search roughly where he is.
In Akane's house, every thing suddenly floats up, including her. Kero figures out it is the work of the Float Card, but Akane giggles when she floats out the window going high in the sky. Kero flies straight up to save her, but he runs out of powers. Luckily, Sakura cathes him falling in the air, and she captures the Float. Unfortunately, a gust of wind prevents her from catching Akane, so she fall down to the ground. Kero descends down to catch her, and Sakura uses the Wood as a shock absorber, so Kero and Akane gets back on the ground safe.
Days later, Akane's mother changes her job to be with Akane all the time. They have to move house, so Akane has to say good-bye to Kero. Sakura offers her to take after him, so Kero gets back home.