Nadeshiko tells Amu that the two should become friends, but Amu sees it as a trick to get her to join the Guardians. Ikuto Tsukiyomi, the mysterious stranger from last time, interrupts the two and attempts to steal the last of Amu's eggs.

Amu joins the Guardians as "The Joker", much to her dismay, and they inform her about the mysterious X Eggs. Ikuto tries to make amends with Amu. A mysterious new teacher named Yuu Nikaidou joins Amu's class.

Amu and Nadeshiko attend Kukai's soccer team practice. One of Kukai's friends, Yamada, is deeply upset when the coach announces he didn't make it to the team. Nikaidou takes advantage of Yamada's feelings and extracts Yamada's Heart's Egg, turning it into an X Egg.

Amu takes her little sister, Ami, with her to a guardian meeting. While the Guardians hold their meeting, the Guardian Characters play with Ami and find a treasure map to a magical egg protected by a dragon.

Amu accompanies Yaya to the guardian's ballet class. During practice, the class's prima Maika Himekawa sprains her ankle and Yaya is chosen to be Maika's stand-in for the upcoming performance. Meanwhile, Nikaidou meets with Ikuto on the street and informs him that that Maika's egg may be the Embryo, but if it is not, Ikuto will need to clean up.

Amu encounters Misaki Watarai, an energetic girl who is also in love with Tadase. After Saaya Yamabuki, head of Tadase's fan club, chides Misaki for Misaki's energetic personality and misunderstanding Tadase's conversation with Nadeshiko, Misaki becomes heartbroken and Nikaidou extracts Misaki's egg, but it hatches into an X Character.

Nadeshiko Fujisaki, queen of the school, invites Amu to tea at the Royal Garden, where she'd meet the Student Council Guardians. However, during P.E. class, the blue egg begins to hatch, and its' Guardian Character runs away!

People view Amu Hinamori as a "cool and spicy" girl; she is actually timid and easily scared. When she wishes to have the courage to show her "true" self, she discovers three colorful eggs -red, blue, and green- in her bed. At school, the eggs draw the attention of Tadase Hotori, the most popular boy in school, who Amu has a crush on.

Nadeshiko invites Amu to a sleep over so that the two can get to know each other better. But in order to keep Ami home, Amu makes up a story about the Seven Mysteries of the Fujisaki house. As Amu arrives at Nadeshiko's home, she begins to believe her own story. Amu and Nadeshiko enjoy their time together, but after Amu takes her bath, she gets lost inside the house. Meanwhile, the Guardian Characters chase a mouse and the ruckus they make terrifies Amu. At night, Amu attempts to sneak out, but she gets lost again. Amu comes across the dance hall where Nadeshiko is practicing for an upcoming performance and Amu thinks that she has failed as a friend for being selfish. However, the housekeeper informs Amu that this was not true. The next morning, Amu is happy that her first sleepover was with Nadeshiko.

Ami wants to decorate a Christmas tree with Amu, so after school, Amu and the Guardians shop for decorations. As the group leaves the store, Yoru steals Su's decoration and Su is separated from the rest of the group. Amu, Ran, and Miki search for Su, but eventually call it a night. Meanwhile, Su befriends a white shaggy puppy who is also lost. The next day, Amu and the Guardians search for Su. Su and the puppy come across an X Egg and the two chase after it. However, Ikuto catches the egg and is about to break before Su prevents him by taking the egg. Utau Hoshina interrupts the confrontation and uses a Character Change to take the egg back from Su. But before Utau can break it, Amu arrives. Amu does a Character Transformation with Su, becoming Amulet Clover and purifies the egg.

The Guardians go to a winter training camp and stay with Kukai's grandfather, who is the priest at a temple near a ski resort. The Guardians enter a snow-sculpting contest, each building a part of a castle. However, Amu becomes discouraged with her gate. When Amu asks Miki to do a Character Change, Miki refuses. On the way back to the temple, Amu asks Tadase about the person he said he already liked when he rejected her. Tadase explains that he was referring to his family's dog. Nevertheless, Tadase confesses that he has come to like Amu's alter ego, Amulet Heart. That night, Amu becomes depressed that Tadase likes Amulet Heart, but that Amulet Heart is not her. Ran reminds Amu that Amulet Heart is Amu's would-be self and that Amulet Heart exists within Amu. Amu then becomes determined to work towards becoming her would-be selves.

Amu goes shopping with Nadeshiko and Yaya for a Christmas party. When Amu sees a music video by Utau, Yaya informs Amu that Utau is a new idol singer. Elsewhere, Utau is practicing her performance, but when she becomes disheartened, her manager, Yukari Sanjo, brings up Ikuto. Utau is then determined to work harder. As Amu hurriedly runs home, she comes to a park where different groups are performing music. Amu hears a sorrowful melody and when she follows it, she discovers that it is Ikuto playing his violin. After the Guardian's Christmas party the next day, Amu returns home. However, the Guardian Characters feel the presence of X Eggs. They return to the park and find that everyone's eggs have been extracted en masse and have turn into X Eggs. In the middle of them stood Ikuto who disappears in a burst of wind along with the eggs.

Amu and the Guardians go to a live New Year's concert where Utau will be performing. While waiting, the Guardians realize that the Easter Company is the sponsor of the concert. Amu also sees Ikuto and follows him into a back area where she inadvertently overhears a conversation between Nikaidou, Yukari, and another person discussing the events that took place on Christmas Eve. As the concert begins, everything is going well until Utau sprouts tiny batwings and four X Eggs appear. The concert ends when part of the scaffolding above the stage falls due to the shenanigans of the Guardian Characters. Amu transforms into Amulet Heart and purifies the X Eggs, but not before Ikuto Character Transforms into Black Lynx and shatters one of the eggs. Amu learns what happens when someone's Heart's Egg is destroyed.

The fifth and sixth graders are being taught how to snowboard by a top snowboarder in Japan, 11-year-old Mifuyu Torii. Amu's Guardian Characters detect that Mifuyu is about to create a powerful Heart's Egg, which also doesn't go unnoticed by Nikaidou. That evening, Mifuyu is about to compete in the preliminaries for a snowboarding competition. However, she becomes scared. When Mifuyu wishes to become brave and break her habit of becoming frightened before competing, her Guardian Egg appears and Snoppe hatches from it. With Snoppe's help, Mifuyu is able to compete calmly in the preliminaries. Nikaidou sees Snoppe and realizes that Guardian Characters are born from powerful Heart's Eggs. Attempting to harness that power, he confronts Mifuyu and causes her to begin to doubt herself. These negative emotions cause Snoppe to turn into an X Egg and Nikaidou quietly makes off with it.

The Guardians learn that Snoppe is missing and set out in search for her. However, there is not much time left before Mifuyu competes. Meanwhile, Nikaidou analyzes Mifuyu's X Egg in a remote cabin, but is interrupted by Suzuki, Amu's admirer. Later, Amu nearly runs into Suzuki and brings him back to the resort where he tells the Guardians about the egg he saw. The Guardians find the cabin, but Nikaidou is alerted to their presence. However, as he slips off, Amu catches a glimpse of him. When the guardians enter the cabin, Snoppe hatches from the egg as an X Character. Amu and Ran transform into Amulet Heart and purify Snoppe. Snoppe returns to Mifuyu and the two are finally able to compete and win the competition. As the group returns home, Amu begins to suspect that Nikaidou is the one creating the X Eggs.

The Guardians meet with child magician Zero, who is also fourth-grade student at the school named Takuya Nakagura. Takuya tells the Guardians about how he loves performing magic. However, as he became more popular, his manager did not want Takuya to perform real magic on stage, instead relying on CG effects. To help, the Guardians organize a magic show where Takuya performs under an alias. After the performance, Takuya talks about an imaginary friend named Zero, who turns out to be his Guardian Character. Amu also confides her suspicions about Nikaidou with the other Guardians. At the studio, Takuya learns that he has been fired, and Nikaidou attempts to turn Zero into an X Egg. The guardians arrive at the studio just in time to see Nikaidou leave, but Zero has already become an X Character. Amu does a Character Transformation with Miki, becoming Amulet Spade and purifies Zero.

Nikaidou plans to use the next X Egg to create the Embryo and selects Kukai as his next target. Meanwhile, Amu is selected as the speech contest representative. The other Guardians lend their aid, but Saaya grows jealous when she sees Kukai and Tadase help Amu. Nikaidou takes advantage of Saaya's jealously and manipulates Saaya into giving Kukai false information about how Tadase was gossiping about Kukai. Soon after, the two guardians are in an argument and Daichi returns to his egg. However, the arguing is a ruse by Kukai and Tadase to bring Nikaidou out into the open. Amu transforms into Amulet Heart and uses the Heart Rod for the first time to stop Nikaidou, but is unsuccessful. Nikaidou escapes, but he tears up Amu's speech manuscript in the process. However, Amu is able to give an extremely short improv speech on friendship and wins the contest.

Tadase invites the other Guardians to an aquarium, however, only Amu is able to go. Amu begins to panic as the trip turns into a date with Tadase but she eventually calms down. As Tadase is about to tell Amu something important, they are interrupted by a little girl who quickly become attached to Tadase. As Amu and Tadase wonder what to do with the little girl, they spot an X Egg floating above the crowd. The egg takes off and Amu chases after it, but the little girl keeps Tadase from following. As Amu is about to catch the egg, she runs into Yoru who is carrying the Dumpty Key. Yoru tells Amu about the Dumpty Key, but the X Egg swoops in and steals the key. Ikuto arrives and chases after the egg with Amu, as Amulet Heart, following. Working together, they finally purify the egg.

On the way home from a park, Amu's parents get into an argument about when they first went on a date. Eventually, they make up, but when they search for the photo Amu's father took when he first met with Amu's mother, they discover that it was missing. Amu's parents get into another argument because Amu's father placed the photo in a bird magazine and Amu's mother donated the magazine to a bazaar. With the help of Nadeshiko and Yaya, Amu searches the bazaar for the magazine and eventually finds it. However, Yoru steals the magazine thinking it contains a clue about the Embryo. Amu chases after Yoru in order to get the picture back, but the picture is torn in the process. Amu and Su transforms into Amulet Clover and use Remake Honey to repair the picture and a broken clock.

Kukai introduces Amu, Nadeshiko, and Yaya to his childhood friend, Sion. Sion is an aspiring pianist and will be leaving town soon to challenge her skills. On the way home from School, Kukai runs into Sion as she searches for a four-leaf clover. The next day, Amu encounters Kukai at a mall as he looks for a farewell gift for Sion. While they look for a gift, the two Guardians run into Sion. Meanwhile, Utau puts on a concert at the mall, and several X Eggs are extracted from the crowd, including Sion's. Amu runs into Utau and meets with Utau's Guardian Character, Il, while Kukai is busy rounding up the eggs. Amu finds Kukai and Character Transforms into Amulet Spade to cleanse the eggs. Just before Sion leaves for her studies, Kukai arrives and gives Sion her farewell gift, a four-leaf clover.

Amu is home alone while her parents go to Ami's school play. Her parents ask her to sign for a crab, that was sent by her grandmother. After a bad encounter with the crab where Miki is caught, Amu goes to meet her parents at a French restaurant. Because Miki is pouting, Amu decides to leave the three at the front of the restaurant. However, Nikaidou steals them. Thinking that they ran away, Amu searches for the Guardian Characters. While searching, she encounters Yoru, who tells Amu that he and Ikuto saw Nikaidou steal Amu's Guardian Characters. Yoru takes Amu to Nikaidou's place, but he leads her through all of the weird cat trails. Amu almost falls off a tall wall, but Ikuto saves her and takes her to confront Nikaidou. Nikaidou is too powerful and he gets away while Ikuto protects her from Nikaidou's powerful X Egg magic.

The Guardians offer to help Amu find her eggs. They run into Utau and Saeki Nobuko, the spiritualist, along the way. Saeki can see the Guardian Characters and is at first frightened by them. However, she agrees to help the Guardians in their search. Utau also comes along because she does not like Nikaidou methods. Saeki drives like a maniac and eventually finds Nikaidou. As the Guardians confront Nikaidou, Utau's manager, Yukari Sanjo, appears and scolds her, asking if Utau is fine with whatever happens to Ikuto. Utau Character Transforms with Il, becoming Lunatic Charm, and attacks the Guardians. Ikuto comes to help and Utau de-transforms upon seeing him. After a struggle, Ran and Miki are freed, but Su is still with Nikaidou. Nikaidou makes a deal with Amu: he will give her a chance to get Su back, but she has to come get Su from his laboratory.

While awaiting Amu to arrive, Su convinces Nikaidou to let her clean up the messy laboratory and make a fresh cup of coffee. While cleaning, Su discovers an old photo of Nikaidou when he was a boy and his mentor. Nikaidou recalls his dream of being a robotics professor and when his own Guardian Egg appeared. However, Nikaidou gave up his dream when his mentor retired due to his wife's illness and Nikaidou's Guardian Egg was broken. Amu arrives at the laboratory, fights a bunch of robots, rescues Su, and purifies all of the X Eggs that Nikaidou had collected. Nikaidou's Guardian Egg reappears and his Guardian Character hatches. The Guardian Character greets Nikaidou, then disappears. Su tells Nikaidou that his "would-be self" can be renewed as many times as needed. Nikaidou stops working for Easter and discovers his mentor did not give up on his dream either.

Amu's class is assigned to draw a composition about their favorite place at school. Amu also learns that Nikaidou has returned to the school as an actual teacher. As she visits various locations around the school, Amu reflects back to the events since her Guardian Characters appeared. When Amu turns in her composition, it is of the other Guardians sitting around the table at the Royal Garden.

Nadeshiko tells the Guardians that she will be leaving for England soon. Meanwhile, Amu is having trouble deciding whether she is in love with Kukai, Tadase, or Ikuto. Amu goes to the Royal Garden to ask Nadeshiko for advice, but finds Nadeshiko is not there. Amu then goes to Nadeshiko's home where she encounters a boy named Nagihiko, who claims he is Nadeshiko's older twin brother. Nagihiko runs off with Amu and takes her for a walk in a park. The two eventually visit a shrine where one can pray to have true love with their loved ones and get matching charms. The two eventually part company. When Nagihiko arrives home, he dresses up as a female and is revealed to be Nadeshiko. It is the Fujisaki family's tradition for the males to be raised as females as part of their dance training. Amu later learns that Nadeshiko is leaving.