On first day for Sakura and her friends at Tomoeda Junior High School, Sakura rejoices upon meeting Syaoran again and learning from him that he had just moved back to Tomoeda. Later that night, after a strange dream, Sakura discovers that all the Sakura cards have turned blank.

During Tomoyo's visit at her house, Sakura, Tomoyo, and Kero become trapped in a closed space. As Tomoyo uses one of her sewing needles to burst it, Sakura uses her staff to capture it the "Siege." That night, she has another dream with the cloaked figure, who attempts to steal her key.

A heavy downpour persists throughout the day, and Sakura captures the card "Aqua." The next day, during Cheerleading Club, Sakura captures the card "Reflect." At home, she meets the cloaked figure in a dream and once again tries to stop it from stealing her key.

Akiho Shinomoto, a student from abroad, transfers to the school, and quickly become friends with Sakura and the others. Later at class, Sakura discovers that the trees at the school grounds are moving by themselves and she captures the card "Action." After school, Sakura meets Yue, who tells her that he can't sense any magic from the new cards. Syaoran contacts Eriol, but he is instructed not to act until the time is right.

Sakura meets her friends for the Flower Viewing, where she is suddenly dragged away by a mysterious force to a large tree in the middle of the forest. She captures the card "Gravitation." Admiring how huge and beautiful the tree is, Sakura convinces her friends to continue their meeting beside it as Syaoran arrives to join them.

Sakura dreams of the cloaked figure again, now sitting atop a clock. The next day, Sakura and her friends borrow the music room during lunch break to hear Akiho and Tomoyo sing together. Syaoran is revealed to know how to play the piano. After the song, Sakura hears a strange noise captures the card "Record", while Syaoran affirms that he had not felt any magic power in the occasion.

Sakura, Kero and Syaoran pay a visit to Tomoyo's house so they can test the powers of Record in the garden. In the occasion she finds a new card called "Flight" and captures it.

Sakura and Tomoyo are invited by Akiho to pay a visit to her new house, which by coincidence is the same mansion where Eriol lived during his stay in Tomoeda, where they are introduced to her butler, Yuna D. Kaito and Akiho shows them her family's vast, personal library. In the occasion, Sakura locates card "Lucid", hidden among the booksheves and capture it. Once Akiho returns, she shows a book in a mysterious language called "Alice in Clock Land" and Sakura can't shake the feeling that the cover's design is somewhat familiar.

Sakura meets Syaoran for a date at the same aquarium where she captured the Watery. At the aquarium, one of the tanks break, flooding the entire room. Sakura ends up trapped underwater by the force of a card until Toya drains the water and Syaoran rescues her. Sakura, along with Tomoyo, Kero, and Syaoran, return to the aquarium at night, where she captures the card "Spiral."

Akiho is paying a visit to Sakura's home when she is put to sleep by the powers of another card. Sakura and Kero chase after it, until they discover that the entire house is surrounded by an intricate labyrinth. After a long chase, Sakura captures the cards "Snooze" and "Labyrinth". After everything gets back to normal, Kaito appears to pick up Akiho and Sakura bids farewell to them.

On their way home from school, Sakura, Tomoyo, Akiho and Syaoran meet Kaito who is returning from shopping. Once back home, Syaoran contacts Eriol, revealing that he sensed some magical power from Kaito, and Eriol suspects him to be a powerful member of an English magician society of dubious repute. Sometime later, Sakura feels the presence of a card and they follow it to the nearby playground where they capture the card "Reversal" with success.

Sakura and her friends participate of the school's sports tournament when a sudden hailstorm occurs. With help from Syaoran, Sakura captures the card "Hail" which is the source of the storm. Later at home, Sakura dreams of the cloaked figure, who is trying to take her key again.

Meiling arrives suddenly in Tomoeda and Sakura receives her in her house. Meanwhile, Yukito and Yue ask Toya about the new power that is growing within him, but Toya claims that it is not the time to reveal it yet. Back at her house, Sakura reveals to Meiling that she knows that Syaoran is hiding something from her, but refrains from asking him about it because she is certain he would not keep secrets from her unless for a good reason. After Meiling reassures her about Syaoran's feelings, the two then prepare to sleep, when Sakura briefly notices some cat ears and tail appearing on Meiling's body. Meanwhile, Akiho confesses to Kaito that she can now read further in her book, and tells him of an event from the book that is strikingly similar to the current situation with Sakura and Meiling.

In the following day, Sakura and her friends gather to visit a shrine, where she sees her friends being turned into animals and transported to a mysterious location. Just as her friends were about to be in harm's way, Syaoran appears to help Sakura, who uses the power of her own will to transport everybody back, and succeeds in capturing the card "Mirage". With Syaoran exhausted from the battle, Sakura concludes that the card acted based on her own thoughts and feelings, and decides that the only way to stop these incidents from happening is by getting much stronger.

Akiho tells Kaito about how glad she was being able to read more of the book, describing the events which occurred with Alice's friends turning into animals, much like Sakura's encounter with the "Mirage" card. Kaito replies cryptically that he hopes Alice will continue to do her best. At Sakura's house, Meiling calls Syaoran on her behalf to check on his health, with Sakura eventually asking him to have adequate rest. Later, Sakura, Meiling and Akiho arrive at Tomoyo's house as she had something to show them: her personal home theater room, where she plays footage from previous plays which Sakura and the others acted in. Halfway through the viewing session, an earthquake shook the house. Using "Snooze" to put Akiho, Tomoyo's mother and her bodyguards to sleep, Sakura and Kero fly above the house to investigate the cause.

Sakura and Kero discover the source of the earthquakes to be a card that is moving underground and prevent it from escaping with Siege, before capturing the card "Swing". After parting ways with Sakura and the others, Akiho meets Kaito on her way home, and as they talk, Kaito lets slip that he knows more about Sakura's father than he should, using his powers to rewind time and make her forget it. On their way home, Sakura and Meiling are attacked by another card and join forces to restrain its movements before capturing the card "Struggle". Before returning to Hong Kong, Meiling and Sakura agree to address each other without honorifics as a sign of their closeness, and as she proceeds to the airport, Meiling contacts Syaoran, affirming that whatever his reasons for returning to Tomoeda are, she will not forgive him if he makes Sakura sad.

Sakura has another dream with the mysterious figure and has a feeling that she finally figured out its identity. During home economic class, the roll cakes start jumping around and fuse into a large monster. Sakura defeats it and captures the card "Appear." Upon returning home, Akiho gives a roll cake to Kaito, who magically puts her to sleep and declares that he shall take all of the Clear Cards from Sakura, with assistance from Momo, when the time is right.

After showing to Akiho and the others the picture book she got from Rika, Sakura and Akiho have another shared dream. Meanwhile, with Syaoran's help, Sakura manages to capture the card "Blaze" and rushes back home, unaware that Toya has already realized that she is not in her room. Yue inquires Toya again about the new powers he obtained, but Toya insists that the time to reveal them has not arrived yet.

Sakura and Akiho take part in a reading session of Buying Mittens for children, and upon returning home, Sakura reveals that she used "Record" in the occasion. However, upon playing what the card recorded, an unfamiliar scene appears. After some investigation, Kero discovers that the scene Sakura recorded was from decades ago, as a sign that her powers had increased to an astonishing level, and after confiding in Yue, they decide that they must contact Eriol at any cost.

Sakura's maternal great-grandfather invites her and Syaoran to his villa on Sunday. However, when Sakura takes a short leave to get more tea, she stumbles upon her mother's room and uses "Record" to view scenes of Nadeshiko (her own mother) when she was a child, when suddenly Nadeshiko's image urges her to stop, stating that Sakura will not be able to return if she delves any further. Sakura and Akiho then have another shared dream, and both Kaito and Momo claim that the time they are waiting for is at hand. Meanwhile, Eriol finally contacts Kero and Yue to explain the situation to them.

After Sakura recovers, her great-grandfather gives her a key originated from England, that according to him, was one of Nadeshiko's most prized possessions. Meanwhile, Kero and Yue are informed by Eriol that he discovered with help from Syaoran's mother that Kaito was expelled from the society of magicians he once belonged to after being held responsible for the disappearance of a mysterious relic with strong magical powers, and somehow it must be a key element in his plan.

Despite having no idea of why Eriol wants to keep secret from Sakura about Akiho and Kaito, Kero and Yue decide to follow his instructions, with Kero standing guard beside Sakura to protect her. However, Sakura and Akiho's shared dreams become more frequent, and both have an ominous feeling about them.