As Pretty Cures all over the world fight against Saiarks, minions of the evil Phantom Empire led by Queen Mirage, Himelda "Hime" Window, also known as Cure Princess, feels downhearted after losing yet again to the Saiark, having to be bailed out by another Cure named Cure Fortune. Blue, the god of the universe, gives Hime a Crystal of Love so that she can find a partner to fight alongside her. Excited to be able to have a friend, Hime decides to randomly throw the crystal to decide her partner, which randomly lands on a girl named Megumi Aino. Hime, along with her fairy partner Ribbon, follows Megumi as she goes about her shopping, helping others when they're in trouble.

Fearing she might lose to the Saiark yet again, Hime decides to escape with Megumi to her hideout. There, Blue explains how the Phantom Empire emerged from a sealed box known as Axia and began plaguing the world with Saiark, including Hime's homeland, the Blue Sky Kingdom. Hime, feeling she has no chance of winning against the Saiark and is a failure as a Pretty Cure, runs off, prompting Megumi and Ribbon to chase after her. Using special items called PreCards to don a magical detective outfit, Megumi, aided by her friend Yuko Omori who had ran into Hime earlier, manages to find Hime and give her some encouragement.

Blue gives Megumi and Hime some Cure Line phones, so they can keep in contact with each other, before urging them to keep their identites as Pretty Cures a secret from their friends and families. However, Megumi has a hard time keeping things a secret from Seiji, who lives next door to her. The next day, during his morning run, Seiji encounters a Newspaper Saiark being led by another one of Queen Mirage's commanders, Hoshiiwa. Arriving on the scene to find Seiji beating up by the Choiark, Megumi and Hime choose to transform in front of him to protect him. After Megumi beats the Choiarks with her new form, Cherry Flamenco, she and Hime team up to defeat the Saiark. Afterwards, the girls, along with Blue, explain their situation to Seiji, who decides to help them out in fighting against the Saiark.

Hime is transferred into Megumi's school under the Japanese name Hime Shirayuki, becoming excited at the thought of making 'one hundred friends'. Upon arriving at school however, she is overcome with fear and finds herself unable to face anyone properly. Megumi tries to get Hime to make friends with Yuko, but she becomes too afraid and turns away from her. Whilst lamenting her actions alone in the gym storage, Hime meets a teacher having his own worries about his students not listening to him. Just then, Namakeruda appears and uses the teacher to create a Cone Saiark. Hime initially struggles against the Saiark, but becomes strengthened by her desire to protect the school and make some friends, defeating the Saiark with help from her new form, Sherbert Ballet. Afterwards, Hime gives the teacher some words of encouragement before working up the courage to become friends with Yuko.

On their way to Megumi's house, Megumi and Hime end up doing a lot of good deeds, such as clearing up litter, treating a injured puppy, helping a lost child, and giving someone courage to propose to his girlfriend. After having pancakes with Megumi and her mother, Hime laments how her parents were trapped inside mirrors by the Phantom Empire, whilst Megumi tells her how she wants to help out her mother, who has a weak body, citing her as the reason she loves helping others. Hosshiiwa takes advantage of Megumi's helping nature to lure her and Hime into a trap, attacking them with a Mole Saiark. As Hosshiiwa passes off Megumi's desire to help others as self-satisfaction, Hime stands by her side, believing in the genuine good feelings from helping others, and manages to break them free from the Saiark and defeat it. Afterwards, Megumi gives Hime her thanks for standing by her beliefs.

Ribbon gets upset at Hime when she doesn't want to eat her home cooking and has lunch at Yuko's house instead. Wanting Hime to understand the feelings behind cooking, Yuko asks her to help out at her family's bento shop, where she learns how much hard work goes into preparing food for others. Just as Megumi brings Ribbon over so Hime can apologize, Namakeruda appears with a Bento Saiark to target the shop. Determined to protect the shop, Hime understands the effort Ribbon puts into her cooking and fights back with her Macademia HulaDance form, allowing Megumi to defeat the Saiark. Afterwards, Hime apologizes to Ribbon for her behavior and the two manage to make up with each other.

As Hime decides to hold a 'special party' at her house, Megumi shows up early with the intention of helping out with preparations. Hime, however, wants to prepare the cake she was making by herself, kicking Megumi and Ribbon out of the house when they try to help her out. As Megumi wonders what exactly she did wrong, Ribbon explains that Hime wanted to prepare the cake herself as a surprise for her. Meanwhile, Hosshiiwa targets a newlywed couple and creates a Wedding Cake Saiark, which Hime attempts to fight on her own, but ends up getting overwhelmed. Megumi arrives in time to protect her, with Megumi apologizing for not understanding her feelings and Hime apologising for getting mad at her.

With the HappinessCharge Pretty Cure gaining popularity thanks to TV coverage, Megumi and Hime attend the local festival with some of Megumi's friends, where Hime ends up spending all of her allowance quickly, but enjoys making new friends. The girls decide to have their fortunes read by Iona Hikawa, a girl from the class next to Megumi's, who foretells a terrible future for Megumi and Hime. Just then, Oresky, another commander from the Phantom Empire, targets Megumi's friends and creates two Matsuri Saiarks, which take the Cures off guard. As the Cures are driven into a corner, Cure Fortune appears and single handedly defeats the Saiarks, before telling Megumi that she is better off not partnering with Hime, believing she can't be trusted.

Lamenting over their last battle, Megumi and Hime decide they need to train their bodies. Seiji takes them to his local karate dojo where Iona also practises, along with Megumi's friend Kazumi. The girls are impatient to learn about the advanced fighting techniques, but Seiji insists they start with basic techniques. The next day, as Kazumi nervously prepares to take an exam to improve her rank, she is targeted by Oresky, who creates a Karate Saiark to attack the dojo. As the Cures rush into attack, Megumi is injured from defending Hime from a feint attack. Just as things look their worse, a mysterious new Pretty Cure named Cure Honey uses a soothing song to put the Saiark under her control and give the Cures the encouragement to defeat the Saiark using the techniques they learnt from Seiji. After Cure Honey takes her leave, Kazumi is encouraged to try her hardest in her exam.

Having been caught on a television broadcast, Cure Honey's song has caught on with almost all of the students, much to the dismay of the choir club president, Hitomi, who wants her club to practise seriously for an upcoming contest. Hitomi becomes upset when the rest of the choir club speak up against her strictness, wanting to perform something for more fun, and becomes targeted by Hosshiiwa, who creates a Music Saiark and uses her own song to spread her chaos, desiring to face Cure Honey. Sure enough, Cure Honey shows up to face Hosshiiwa in a vocal showdown and comes out as the winner. Cure Honey then shows off the power of her Honey Baton to help Megumi and Hime defeat the Saiark. Afterwards, as Hitomi makes up with the choir club, choosing to go with Cure Honey's song for the contest, Yuko reveals to Megumi and Hime that she herself is Cure Honey.

Blue explains that he gave Yuko the power to become a Pretty Cure prior to Megumi, though Yuko decides to withhold telling her secret right away. The next day, Yuko invites Megumi, Hime, and Seiji to the mountains, where they all help Yuko's grandparents plant rice used in her family's restaurant. Although Hime is eager to know why Yuko kept quiet about her identity, she comes to understand more of Yuko's kindness. Just then, Namakeruda appears and targets Yuko's grandparents to create a Scarecrow Saiark, with Megumi and Hime unable to fight easily in the mud. As Yuko joins the fight, she discovers the Saiark is resilient to her song, but she is soon supported by Megumi and Hime and manages to defeat the Saiark with her Popcorn Cheer form and her Honey Baton. Afterwards, as the girls eat the rewards of their work, Yuko explains the feelings behind delicious are the reason she became a Pretty Cure, revealing she was too embarrassed to come forward before.

Megumi ends up ranking in the bottom two in her class and has to take a retest or else face after-school lessons for the rest of the school year, along with her classmate Kenta, who is more interested in baseball than studies. Megumi is put under further pressure when Blue threatens to suspend her from Pretty Cure activities should she fail her next test. Whilst Hime and Yuko help Megumi with her studies, Seiji teaches Kenta the importance of studying. On his way home to study, Kenta is targeted by Namakeruda, who creates a Baseball Saiark which Megumi challenges to a baseball match. After a series of foul balls, Megumi manages to figure out the pattern of the Saiark's pitches and land a home run, allowing her to defeat the Saiark. Afterwards, Megumi and Kenta study hard and manage to pass their retests.

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As Phantom continues to defeat Pretty Cures across the world, Megumi worries that Phantom is too powerful for her and the others to handle. Deciding to put it behind her for now, Megumi and the others help out Mao's class, including a superhero obsessed classmate named Takuma, on a trip to the beach to collect clams. As the group help Takuma search for clams, with Takuma later helping out others, they are targeted by Oresky, who summons a Clam Saiark. Spurred on by Takuma's hero spirit, the Cures overwhelm the Saiark and save the day, allowing the kids to enjoy their spoils.

On Mother's Day, Megumi and Yuko suggest to Hime that they travel to the Blue Sky Kingdom so she can deliver specially made cakes to her mother, who became trapped in a mirror when the Phantom Empire invaded. Blue allows the girls to go, but warns them to avoid battles as much as possible, as their Pretty Cure powers will be weakened due to the Phantom Empire's influence. Arriving in the Blue Sky Kingdom, the girls use their Ninja outfits to avoid detection by the Choiarks as they make their way towards the palace, where they have to get past several Knight Saiarks. After using a hidden passageway, the group arrive at the throne room where Hime's imprisoned parents are. After delivering Hime's cakes to her mother, the girls transform to escape, but are soon discovered by Hosshiiwa, Namakeruda, and Oresky, who send a trio of Saiarks after them.

Megumi and the others become concerned when newscaster Miyo Masuko announces on her Pretty Cure Weekly report show that she will unveil the secret identities of the HappinessCharge Pretty Cure. Things only worsen when Miyo shows up at their school, believing the Cures to be students at the school, and starts following the girls everywhere, even showing up at Megumi's house. After Megumi gives her a taste of her own medicine, Miyo explains how she was once saved by a Pretty Cure and desired to become one herself, becoming a reporter to learn more about them.

Wanting to support Seiji as he participates in a karate tournament, the girls decide to make him lunchboxes, which Hime isn't particularly skilled at. Whilst out shopping for ingredients, Hime encounters Seiji practising his karate, becoming curious as to why he works so hard at it. Just then, Oresky targets another karate student and created a Karate Saiark, with Seiji offering to help hold off the Choiarks for Hime. As Megumi and Yuko come to their aid, Seiji explains that it was Megumi who inspired him and Yuko to keep doing their best, giving Hime the encouragement to work hard too and defeat the Saiark alongside Megumi. Afterwards, Hime gives her all to make some omelettes for Seiji, who manages to win his tournament.

Yuko and her family are asked to cater for a wedding between two customers, Sachiyo and Daisuke, with Megumi and her friends offering to help out with preparations and Hime suggesting they use the theme of 'four somethings' for the bride's outfit. However, Sachiyo informs the group that her best friend who was supposed to give her 'something borrowed', Iona's older sister Maria, has gone missing, so the girls ask Iona to deliver it in her place. On the day of the wedding, after Iona gives Sachiyo Maria's handkerchief, Hosshiiwa crashes the wedding and creates a Bride Saiark from the newlywed couple. Determined to protect the wedding, Cure Fortune appears and leads the Cures to victory, allowing the celebrations to continue.

As Megumi and the others are disappointed to learn from Ribbon that only one of their wishes upon completing the PreCard File, Cure Fortune's partner, Glassan, suggests to Cure Fortune that she team up with the HappinessCharge Pretty Cure, but she outright refuses as she still can't bring herself to join forces with Hime. Later that night, Hime becomes defiant when Blue and Ribbon propose telling Megumi and Yuko about the Axia Box, fearing that she would lose her friends if they knew her secret.

Despite offering to team up with Megumi and Yuko, Iona refuses to work with Hime, revealing that she is the one who opened the Axia Box and released the Phantom Empire, blaming her for the defeat of Maria, who was Cure Tender. Unable to face Megumi and the others with her secret revealed, Hime runs away, prompting the others to search for her.

Hime secludes herself in her room, believing Megumi has ditched her in favor of Iona, who continues to reject Megumi's offer of joining the team due to her hatred towards Hime. Megumi and Yuko use food to lure Hime out of her room, using their PreCards to chase after her when she tries to escape, reminding her of their strong friendship and assuring her that the opening of the Axia Box wasn't her fault.

After Megumi's group manages to defeat all of the Saiarks in Pikarigaoka, they are approached by Glasan, who informs them that Iona had disappeared, prompting the Cures to search for her. Upon learning that Iona is trapped in another dimension, Blue calls the Cures to the Cross Mirror Room to combine their feelings of wanting to help her. Meawhile, Iona is overwhelmed by Phantom, who takes the Pretty Change Mirror she got from Maria and burned up her transformation PreCards, sending her into despair.

Mirage attempts to attack the Cures but is stopped by Blue, who attempts to reason with her, only for his words to fall upon deaf ears, forcing the Cures to retreat when Mirage attempts to attack Megumi. Arriving back home safely, the girls decide to put together a party to celebrate the complete formation of the HappinessCharge Pretty Cure.

Iona suggests to the others that they hold a training camp at the beach to make their team stronger. After Iona has each member practise their special moves, which looks like typical playing to the normal eye, the girls try to come up with a new group pose, during which Megumi gets soaked by a wave, before winding things down with a beach volleyball match. They then coincidentally encounter Oresky, who was undergoing his own beach training, and use the results of their training to defeat his Lighthouse Saiark. Later that night, as Megumi comes down with a fever, Seiji feels conflicted when he sees Blue carry a blushing Megumi to her room.

Whilst Blue looks after Megumi, who is still sick with her cold, he is asked about his feelings concerning fighting Mirage. Hime invites some of her friends to join them in their training, one of whom, Rin, has a crush on Seiji. As Megumi recovers in time to join the others for a barbecue, Hime is helped out by Seiji after a plan to play a prank on him goes wrong. Just then, Namakeruda appears and targets Rin to create a Love Saiark, which the Cures manage to defeat. Later that evening, Rin confesses her feelings to Seiji, but is rejected as he already likes Megumi, something which the girls agree to keep secret from Megumi.