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.

Syaoran's feelings for Sakura have been steadily increasing, though he still doesn't understand why, and Sakura remains blissfully unaware of it. Soon Sakura invites him to go to a teddy bear festival with her, Tomoyo, and Eriol. However, Eriol secretly traps Sakura and Syaoran on an elevator, where the two grow closer. Eriol then creates a large hole in the wall of the elevator, causing Sakura to fall through. Distraught, Syaoran calls out to Sakura by her first name for the first time.

Eriol casts a spell on Kerberos and Yue so that they are unable to revert to their guise forms, much to Sakura's dismay, since it is understandably difficult to hide their true forms for long. Fortunately, Toya and Fujitaka are out for the day, and Sakura has them help around the house while reminiscing about their time with Clow Reed.

Sakura grows in magical strength and power for every Clow Card she transforms into a Sakura Card, while Yue's energy begins to falter. Yue also comes to the realization that Eriol is in fact Clow Reed and transforms in front of him. However, Eriol makes Yukito faint and erases his memory of him ever realizing who Eriol truly is; Clow Reed, since he is not yet ready to reveal himself and also reverses Yue's transformation back into Yukito. Syaoran, in the meantime, has fully realized his strong romantic feelings for Sakura and consults with Tomoyo, who helps him deal with his jealousy towards Eriol and gives him the confidence (just barely, though) to speak his mind to the oblivious Sakura. Before he can do so, however, both he and Sakura sense Clow Reed's presence once again, this time in the form of a basketball that leads them through the school at night.

Remembering his promise to Meiling that he would be her "fiancé" until he found someone he loved more, Syaoran calls her to tell her that he is in love with Sakura, though he is taken by surprise when Meiling arrives in Tomoeda for the day. While Meiling spends the day with her old friends, the group is attacked by a set of enchanted penguin statues at the playground.

Kero is almost positive that Toya knows everything about Sakura's secret, though Sakura dismisses his claims, saying Toya would make fun of her if he did. Toya, meanwhile, is certain that Nakuru is deliberately interrupting him while he tries to tell Yukito the truth about why he is always feeling fatigued. The two make plans to buy a Christmas present for their father, though Sakura senses Clow Reed's presence again.

Sakura goes to a New Year's festival and notices that Yukito isn't around. Toya goes to check on him, discovering that he has not only collapsed from fatigue, but he's also beginning to fade from existence since Sakura's power, despite how strong it has become, is not enough to sustain Yue. Later at the festival, she receives a fortune from Eriol which he secretly made and enchanted, saying that she will begin to learn the "truth" in her "first dream of the year."

Sakura and her friends go spend the day at a new indoor water park, where Eriol causes the water to rise to dangerous levels. When Rika, who has trouble swimming, nearly drowns, Sakura uses the transformed Watery card to save her, risking being seen using her magic by everyone.

Sakura's class goes on a field trip to the mountains for skiing lessons. At the lodge, Syaoran admits to Sakura that the person he cares for most is not Yukito, and that his attraction to him was actually his reaction to Yue's power; however, he still can't bring himself to tell Sakura that she is the one he's in love with. The next day, Sakura goes up the mountain with Eriol when a blizzard begins to form. At the top of the mountain, there is an avalanche that threatens to bury the lodge at the foot of the mountain where their classmates are.

Toya and Yukito are starring in an independent film directed by Nakuru for their school fair, and Nakuru gives Sakura a role. Sakura later begins to notice that Yukito is losing his power and is starting to fade away. Things come to a head when Yukito passes out and falls of a veranda while shooting the film, though he is saved by Toya and, secretly, Sakura. Toya finally manages to tell Yukito the truth about his power, telling off Nakuru when she attempts to interfere. In order to maintain Yue's power and existence, thus allowing Yukito to survive, Toya sacrifices his powers to save him, though losing the ability to sense when Sakura is in danger.

After viewing Nakuru's film, Sakura tours the high school fair with her friends, while Toya comforts Yukito when he appears troubled by the fact that he is not human. Alone with Yukito in one of the attractions, Sakura tells Yukito how much she likes him. However, Yukito gently rebuffs her, saying that her love for him is merely fatherly, quite similar to her deep feelings she has for her father, and that he already has someone he really likes and cares for a lot. Sakura, in a rare moment of insight, realizes that person to be her older brother, Toya. Yukito tells Sakura that the person she really likes most is still out there when Sakura senses Clow Reed's presence once more.

Sakura heads to school in the morning, but does not see Yukito. She notices that there is a festival and asks Syaoran whether he wants to go to the festival at Tsukimine Shrine. He agrees, much to Sakura's delight. As the lessons continue, Sakura feels sleepy again. Syaoran notices this and is worried. As Tomoyo and Sakura walk home, Sakura admits that she feels much better now and thanks Syaoran and Tomoyo for their help. As Syaoran and Sakura walks to the shrine, Sakura gives Syaoran her handmade scarf, which Syaoran shyly accepts.

Wondering what will happen once all the Clow Cards have been transformed, Sakura uses the Return card to travel back in time to talk with Clow Reed. Sakura meets with Clow Reed and he answers her questions, but during the experience, Sakura realizes that Clow Reed's house is the same one that Eriol is now living in.

Eriol reveals his true identity to Sakura and Syaoran to be the reincarnation of Clow Reed's spirit. He sets his final challenge: turn all of the remaining Clow cards into Sakura Cards or the world will remain in eternal sleep and darkness. Sakura manages to turn six of the eight cards into Sakura Cards except for the Light and Dark ones, because both cards are loyal to Clow Reed and she is not powerful enough. Kero and Yue both help out Sakura by embedding their power into her staff, however if Sakura still fails then they will remain asleep in the staff forever.

Sakura ponders over Syaoran's confession and is confused of her own feelings for him. Meanwhile hearing word that Eriol is leaving for England, they decided to visit his house for an explanation. While there, Eriol explained that the cards needed to be handed over to the new owner, but without a reason the cards would run amuck. He refused to reveal his identity sooner because he knew Sakura would do her best if she didn't know what was going on.