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.

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.

The school year ends, but Amu is depressed because Nadeshiko has left and Kukai will be graduating. To help cheer her up, Kukai teaches Amu a new move for Amulet Heart. Later that night, Ikuto wanders the streets and gets into a fight with two guys who were harassing two girls. Amu is also out shopping to cheer herself up, but she overhears the two girls as they escaped, talking about a guy with cat-like reflexes. Worrying if it was Ikuto, Amu searches and finds him in an alleyway. After Amu tries to treat his wounds and gets teased in return, Ikuto leads Amu home. Along the way, they stop at an amusement park that will be torn down soon. After riding several of the rides by herself and with the Guardian Characters, Amu finally gets Ikuto on a tea-cup ride where the two share a heart to heart moment.

A new school year begins and Amu wakes up to find a yellow Guardian Egg with a diamond pattern in her bed. Meanwhile, Utau steals more Heart's Eggs during a concert. This results in an argument between Il and Utau's second Guardian Character, El, causing El to fly away. Amu is excited that she and Tadase will be in the same class, but being in a new class makes her nervous. The class gets excited over a transfer student, Rima Mashiro. Ran, Miki, and Su sense another Guardian Character coming from Rima. However, when Amu's unsuccessfully attempts to become friends with Rima, a rivalry between the boys, who support Rima, and the girls, who support Amu, breaks out. The rest of the day fares no better as Amu has trouble capturing an X Egg, nearly hitting Yaya in the process. Amu becomes depressed, and her fourth Guardian Egg turns into an X Egg.

Amu tries to catch her X Egg, however she literally bumps into El and takes El home. The next day, the new Guardians are announced. Rima is the new Queen's Chair and Kairi Sanjo is the new Jack's Chair. The new Guardians introduce themselves, but things starts off roughly and Amu is unable to tell anyone about the diamond egg. To deal with the rise in X Eggs, Tadase decides that the other guardians will help Amu by splitting up into teams and search for them. Amu is first paired with Rima and the two eventually find an X Egg. However, Amu is unable to capture it. Rima and her Guardian Character, Kusukusu, Character Transforms and become Clown Drop. Instead of purifying the egg, they destroy it. Amu becomes upset with Rima even though Rima does not understand why. Meanwhile, Ran and El talk about what happened between El and Utau.

Kukai comes back to visit the Guardians. He notices that Amu is feeling down, so he decides to ask her what is wrong. As they talk, they encounter Utau. Utau shows Amu that she has Amu's diamond egg. Utau tries to goad Amu into a fight, but Amu refuses. With the power of the Humpty Lock, El does a Character Transformation with Amu, becoming Amulet Angel, and Kukai does a Character Transformation with Daichi, becoming Sky Jack. Diamond hatches from her X-egg and does a Character Transformation with Utau, becoming Dark Jewel. Nevertheless, Amu's and Utau's Character Transformations do not last long and they are both exhausted. Ikuto appears and apologizes to Amu for Utau's actions. Utau becomes furious that Ikuto is taking Amu's side and forcefully kisses him twice. Ikuto gets angry, and tells Utau to stop because they are siblings, to the surprise of Amu and Kukai.

The Guardians attempt to capture an X Egg, but Rima destroys it instead. Amu scolds Rima for not following the plan, but Rima thinks that Amu's methods are foolish. The next day, the Star and Moon classes are competing against each other in an athletic festival. Rima sits out since she does not see the point in getting all sweaty. When a girl in the Star Class is injured, Amu convinces Rima to take her place. However, Rima still does not want to participate. Another X Egg appears and Amu transforms into Amulet Heart and chases after it. Amu chases the X Egg out onto the athletic field in front of the entire school. Fortunately, everyone mistakes it for a cheerleading routine, and Amu purifies the egg, to the amazement of Rima. After the festival, Kairi informs his sister, Yukari Sanjo, about the events.

Yaya convinces the Guardians to hold a special meeting at her house. It turns out that Yaya just wanted the Guardians to help babysit her baby brother, Tsubasa, because she does not want to. Yaya is jealous of her brother because he is always the center of attention instead of her. When Utau becomes the suspect in the rise of X Eggs, El interrupts the meeting. Amu tries to explain about El and her fourth egg, but Tsubasa begins to cry. Amu is the only one who knows how to take care of a baby. As the group is about to leave, Yaya discovers that Tsubasa is running a fever and become frantic. She rushes him to a doctor who gives Tsubasa some medicine to bring down the fever. Afterwards, the doctor compliments Yaya for being a big sister. Later, Amu finally tells the Guardians about her egg.

When Rima gets stuck with organizing the class's book collection, Amu stays behind to help out. Rima asks Amu to call her by her first name, and vice versa. While cleaning, Amu finds a popular gag comic, which Rima grabs and speedily reads. As she reads, Rima does a Character Change and cracks a joke in front of Amu. Embarrassed, Rima tells Amu not to tell anyone that she loves gag comics. Amu runs into Kairi and learns that Rima was nearly kidnapped before and there was a dispute between her parents. The next day, Rima accidentally Character Changes and cracks a joke in front of the entire class. Afterwards, Rima runs out of classroom and Amu chases after her. Amu tells Rima that a similar incident happened to her, referring to Amu's first Character Change. The two girls have a heart to heart and become best friends.

Tadase and Amu go shopping together as Kairi follows them in order to spy on Amu. Amu sees a bracelet that she likes, but Tadase buys Amu a black heart-shaped barrette. Tadase buys himself and Amu ice cream, but Amu's ice cream drips onto her skirt and he runs off to go find a fountain to wet his handkerchief. Ikuto drops by and teases Amu. Amu becomes angry and ends up tripping on one of the shopping bags, falling onto Ikuto. When Tadase returns, a fight breaks out between him and Ikuto. Kairi and El arrive and El forces Amu into a Character Transformation, much to everyone's surprise. However, Amu's effort to stop the fight is ineffective. Tadase and Ikuto continue their fight and eventually Ikuto runs off with Tadase chasing after him. Kairi, who had been watching the whole thing, gives Amu the bracelet she had wanted and then runs off.

The Guardians decide to investigate a house that is alleged to be haunted. However, Amu is scared of ghosts and does not want to go. Rima bumps into a boy at school who drops a small photograph of his family. The next day, the Guardians arrive at the house and begin their investigation, but Amu is frightened out of her wits. Ran, Miki, and Su chase after what they think is a ghost, but turns out to be a Guardian Character, Kuuta, who is fading away. Meanwhile, Rima sees the boy she bumped into the day before, Shouta, enter the house and she returns the photo to him. Shouta's dream was to be a painter. However, his parents argued over it and his grandfather, who supported Shouta's dream, died. Shouta's depression causes Kuuta to turn into an X Character. Working together, Rima and Amu Character Transform and purify Kuuta.

Amu's family receives a wedding invitation from Amu's cousin, Shuu. They go to the hotel where Shuu works and Amu finds him in the kitchen. Shuu's dream is to be a patissier and he is excited about his wedding and making his first wedding cake. When Shuu's fiancée, Eriko, arrives, Shuu sticks his foot in his mouth and earns a slap from Eriko. It appears that the wedding may be called off. To repair the situation, Amu appears in front of Eriko as Amulet Angel, but falls down. Eriko tells Amu about when she fell in love with Shuu and that she has no intention of calling off the wedding. However, Shuu's egg has become an X Character and Amu transforms into Amulet Clover and purifies it. Shuu, Eriko, and Amu make a new wedding cake together and the next day, the wedding goes without a hitch. When Eriko throws the bouquet, Amu catches it, and suddenly, Kairi, Kukai, Tadase, and Ikuto come into mind.

Shuraiya, a prince from a faraway country, makes a grand entrance to Seiyo Elementary to search for his future queen. Shuraiya also has a Guardian Character, Ramira. After seeing Amu transform into Amulet Heart and purify an X Egg, Shuraiya proposes to Amu. However, Amu refuses. Shuraiya informs the Guardians that the real reason he came to Seiyo Elementary was to find the Embryo. Shuraiya is searching for the Embryo because he despises his father and wants to succeed at something his father failed. Unable to obtain any information from the Guardians, Shuraiya demands to see Utau because she works for Easter and may know more about the Embryo. When Yukari learns of this from Kairi, she forms a plan using Nikaidou's old research. Later that night, Utau appears in disguise and hands the prince a pendant telling him that it is what he seeks.

The pendant Shuraiya receives from Utau begins to change his personality. Pearl, Shuraiya's servant since childhood, finds Ramira suffering because of the pendant's dark energy. She brings him to the Guardians and tells them that she has been able to see Ramira. Ramira informs the guardians about what happened the night before. Meanwhile, Shuraiya extracts Saaya and her followers' eggs, which become X Characters. When the Guardians arrive, their Guardian Characters are captured and Ramira is turned into an X Egg. Pearl protects Ramira's egg to keep from turning into an X Character and explains to Shuraiya that his father cares for him deeply. Pearl's strong feelings give birth to her own Guardian Character who frees the other Guardian Characters. Amu and Rima transform and purify the X Characters and Ramira. Shuraiya apologizes to Pearl for his action and decides to return home and reconcile with his father.

Yukari tells Kairi to obtain the Humpty Lock from Amu. During a meeting, Kairi stares at Amu and the other Guardians believe he is in love with her. The next day, the Guardian Characters hold a secret meeting and El brings the lock with her. When Il and Yoru show up, a fight erupts. Amu and Kairi find the Guardian Characters and Kairi obtains the lock. Tsukumo, who works under Yukari, steals the lock from Kairi and runs off. Ikuto appears, praises Kairi for his "good job", and goes after Tsukumo. Amu attempts to Character Transform, but cannot without the lock. Ikuto, as Black Lynx, catches up with Tsukumo and stops him. When Amu catches up, the Humpty Lock and the Dumpty Key react. Ikuto tries to open the lock with the key, but Amu becomes scared and the lock rejects the key. Ikuto returns the lock to Amu and leaves.

Easter is implementing its new project, the Black Diamond CD. It is rumored that a person will have their wish granted if they listen to it. Kairi slips one of the CDs into Tadase's bag. Tadase and Kiseki get into an argument and Kiseki runs off. At home, Tadase finds the CD in his bag. When Kiseki returns, he finds Tadase listening blankly to the CD and Kiseki becomes an egg. Kiseki goes to Amu for help and they find Tadase with a group of other children around a van playing the song from the Black Diamond CD. The music extracts X Eggs from everyone and an X appears on Kiseki's egg. Amu snaps Tadase out of his depression, and Tadase and Kiseki Character Transform into Platinum Royale. Together, they round up the X Eggs and purify them. Among the eggs, one sparkles more brightly then the others and disappears.