Hoshina Hikaru is a second-year middle school student who loves space! One night, as she was drawing some constellations, she met a mysterious fairy. She got warped to space for a little bit before waking up the next morning, thinking it was all a dream. But it wasn't so, so Hikaru proceeds to name the fairy "Fuwa". She meets two aliens: Lala and Prunce who came to Earth to find Fuwa but a bad alien, Kappard had followed them to get Fuwa first. But Hikaru transformed into the legendary warrior, Cure Star to protect Fuwa.

The rocket that Lala and Prunce were operating had gotten some damage, so Lala decided she'd try to repair it. Hikaru is surprised to hear Lala is 13 years old, like herself, but that Lala is also considered an adult back at home. At the same time, Lala was secretly upset that she couldn't become a Pretty Cure as well. As if he heard her doubts, Kappard appeared and was too tough for Star to handle on her own. So Star sends encouragement to Lala who was defending Fuwa. This helped give Lala some courage that led to her debut as Cure Milky!

Prunce deduces that the noise from the Star Color Pendant is related to the Star Princesses. As Hikaru tries to find where the noise leads to, she ends up butting heads with Lala, who wants to wait until her data analysis is complete. After receiving some advice from Elena Amamiya, a florist who is popular at Hikaru's school, Hikaru and Lala learn to stop arguing and listen to each other properly. Upon figuring out that the pendant is acting as a radar, the girls find a Star Color Pen, but it is swiped by another Notraider commander, Tenjou. With Tenjou defending herself with her Notray troops, Hikaru relies on Lala's help to get her through Tenjou's defenses and recover the Taurus Princess Star Color Pen. Using the pen's power, Fuwa revives the Taurus Star Princess, who urges the girls to help Fuwa grow and retrieve the other pens in order to save the universe. In the end, Hikaru and Lala apologize for their bad behavior and are forgiven.

Lala comes to Hikaru's school, where she observes how much everyone admires Elena for her sporty prowess. After briefly running into student council president Madoka Kaguya, who notices something peculiar about them, Hikaru and Lala go to thank Elena for helping them make up for their fight at her family's flower shop, where she looks after her many siblings. On their way home, Hikaru and Lala come under attack by Tenjou, who uses a smokescreen to keep them separated from each other. Having noticed the commotion, Elena rushes in to protect Fuwa, who gives her the power to transform into Cure Soleil and face Tenjou.

Madoka ends up discovering Fuwa and becomes conflicted over whether she should report her to her father Fuyuki, who is chief of the Diet's Space Research Special Task Force. As Hikaru and the others try to convince Madoka to stay quiet, they come across Tenjou, who attacks with overwhelming numbers of Notreys. Prioritising her own feelings over her father's wishes, Madoka strives to protect Fuwa and gains the power to become Cure Selene. After beating back Tenjou, Madoka keeps everyone's identity a secret from Fuyuki and vows to fight as a Precure.

With Lala struggling to repair her rocket, Hikaru takes her to the local observatory, where a man named Ryo studies the stars, in the hopes of taking her mind off of things. As Lala remains defiant, Ryo shows her his planetarium, teaching her about constellations and relationships. Just then, another Notraider commander named Eyeone uses the power of a Dark Pen to turn Ryo's imagination into an evil monster known as a Notrigger. Realizing the meaning of Ryo's words, Lala relies on the help of the other Cures to retrieve the Dark Pen and convert it into the Leo Star Color Pen, allowing her to defeat the Notrigger, save Ryo, and revive the Leo Star Princess. Afterwards, Lala asks for everyone's help in repairing her rocket.

As the girls begin repairing the rocket with roles assigned by the AI, Hikaru comes up with an idea on how to make the rocket look cuter. Intrigued by Hikaru's design, Lala goes against her AI's predetermined plan and works with everyone to decorate the ship, with the AI noticing how cheerful these logically unnecessary actions are making Lala. Tenjou appears and sends her Notrays to try and smash the rocket, but the Cures manage to protect it and beat her off. With their rocket fully completed, the girls head off into space to search for the next Princess Star Color Pen.

The girls arrive on the planet Kennel, where they meet three dog-like aliens named Doggy, Maggy, and Neggy. There, they discover the Libra Star Color Pen being treated like a sacred treasure by Doggy's people, leading Elena and Prunce to clash over whether they should take it from them. As Kappard arrives to try and take the pen for himself, Prunce, prioritising Elena's safety above all else, uses a fur-growing potion to protect Doggy's group as they retrieve the pen, allowing Elena to defeat Kappard. Afterwards, the planet's elder, having fixed the planet's true treasure, allows the pen to go with the girls, who revive the Libra Star Princess.

Worried that her father is close to finding out about Precure, Madoka's stress over maintaining her perfect image leads her to start making mistakes. Noticing her worries, Hikaru and Lala take Madoka to the shopping district for the first time to try Star Donuts for the first time. Just then, Eyeone targets rival classmate Sakurako Himenojo to summon a Notrigger. Supporting her fellow Cures, Madoka retrieves the Capricorn Star Color Pen, allowing her to rescue Sakurako and revive the Capricorn Star Princess.

After hearing about the Southern Cross from Ryo, Hikaru decides to search for it, only for everyone's attention to turn towards another Star Color Pen on Kumarin, a planet with twice the gravity of Earth. Guided by a resident named Kumu, the girls are soon confronted by Kappard, Tenjou, and Eyeone, who have received a power boost from their leader, Darknest. As the Cures become overwhelemed by their opponent's new strength, losing both the new Star Color Pen and the Taurus Pen in the process, Fuwa and the others help them make an emergency retreat back to Earth, landing near where Fuyuki is searching.

Escaping from Fuyuki's party to the observatory, the group is discovered by Ryo, who keeps them hidden from Fuyuki and agrees to keep Lala and the others a secret. While Ryo consoles Hikaru as she blames herself for what happened, Eyeone uses the Taurus pen to turn herself, Kappard, and Tenjou into a Notrigger, which attacks Fuyuki. As Hikaru struggles against the Notrigger, she receives encouragement from the others, allowing her and the others to call upon the power of the Twinkle Sticks, letting them defeat the Notrigger and recover the Taurus pen. After the Notraiders escape, Hikaru's group is confronted by Fuyuki when they are approached by a man with a camera.

The man, revealed to be film director P.P. Abraham, tells Fuyuki that everything is part of a movie, which he ends up having to actually film after Hikaru and the others try to play along. As Abraham, who reveals himself to be an alien in disguise, states that Lala and the others will be sent home for breaking space laws, Hikaru vows to make his movie a success in exchange for letting them stay. Although the girls initially struggle with following the script, Hikaru and Lala's honest feelings over not wanting to part with each other moves Abraham. Just then, Eyeone uses a Dark Pen on Abraham to summon a Notrigger, but the Cures manage to defeat it. Moved by Hikaru's friendship, Abraham allows Lala to stay on Earth, giving her the Earth name Lala Hagoromo.

To go to school is Lala's dream! By removing the A.I. out of her life, Lala's common sense starts to falter at school, leaving her puzzled and losing sight of herself...

The girls come over to Elena's house and are introduced to her family, learning about their Mexican heritage and their love of song and dance. However, Elena's brother Touma gets upset and runs off the next day, believing that his family is weird. Catching up to Touma, Lala teaches him that the ways different cultures act isn't inherently weird. Just then, Tenjou, who has retrieved the Scorpio Star Color Pen, appears and transforms Touma into a giant Notray. Stating her love for her family despite its weirdness, Elena manages to recover the Scorpio pen and rescue Touma, reviving the Scorpio Star Princess in the process.

The girl's search for the Sagittarius Color Pen leads them to an auction on Planet Zenny, which they manage to attend thanks to an invitation by space idol Mao. When the pen is put up as an auction item, Madoka uses donuts brought in by Pruns as currency to win the audition. However, the pen gets stolen by Mao, whose true identity is revealed to be that of the space phantom thief Blue Cat. When Eyeone appears with another Notrigger, Blue Cat decides to give the pen to Madoka so the Cures can defeat it and revive the Sagittarius Star Princess.

Madoka takes part in the finals of the national archery tournament, determined to succeed for her father's sake. However, she is pressured by rival archer Yumika Nasu, who claims that spending time with her friends has made her weak. Wanting to help her, Hikaru and the others make matching Fortune Capsule charms to encourage her. Just then, Yumika, who was actually just feeling lonely, is turned into a Notrigger by Eyeone, but the Cures manage to defeat it and rescue her. Afterwards, Madoka's support from her friends allows her to beat Yumika and win the tournament.

The girls return to Planet Zenny in order to retrieve the Virgo Color Pen when they run into Blue Cat, who was planning on robbing the house of the rich celebrity, Dramus, which just so happens to be the location of the pen. The girls work with Blue Cat as Dramus puts them through several traps within his house in order to take the rest of the pens, but Blue Cat's intellectual nature helps them reach his lair of treasures. As Blue Cat is mesmerized by the treasures of Planet Rainbow, Dramus attempts to destroy them but the Cures vow to protect them. Kappard suddenly appears and tries to steal the pen by targeting Dramus to power up his weapon, but Blue Cat distracts him, allowing the Cures to defeat him. A grateful Dramus allows the pen to go with the Cures and they revive the Virgo Star Princess. But unbeknownst to them, Blue Cat is revealed to have an agenda regarding the Star Color Pens.

Hikaru's mother Terumi, who works as a manga artist, is chosen to draw one-shot manga for a magazine with the hopes of getting serialized. As Hikaru and the others decide to help Terumi out as her assistants, Terumi's editor pushes her to draw a romance manga, feeling sci-fi or fantasy, the genres she excels at, won't sell. Although Terumi manages to finish the one-shot on time, she becomes downhearted upon learning it is being poorly received by the publisher, leading her to become targeted by Tenjou and turned into a Notray. Remembering the fantasy manga that Terumi drew for her as a child, Hikaru rescues Terumi and encourages her to aim for serialization with a fantasy story. Meanwhile, Blue Cat manages to get ahold of a Star Color Pen.

The girls arrive on Planet Rainbow and find its feline denizens petrified before finding Blue Cat's treasure stash where a Star Color Pen awaits. But are soon followed by Eyeone, who reveals herself to have turned the planet's citizens to stone while experimenting with the Aries Dark Pen. Eyeone manages to capture Fuwa in the battle that followed, Fuwa smelling a familiar scent from Eyeone's butler Bakenyan. It is then that Bakenyan reveals himself to be Blue Cat in disguise, the thief revealing herself to be a resident of Rainbow who infiltrated the Notraiders to steal the Star Color Pens from them. A furious Eyeone uses a Dark Pen to turn one of the petrified citizens into a Notrigger, leading Lala to deduce that they still possess hearts and can be restored as Blue Cat uses a flash grenade to keep Eyeone from stealing the Gemini Star Color Pen. The Cures defeat the Notrigger and revive the Gemini Star Princess sisters, offering to help Blue Cat.

The Cures catch up to Blue Cat as she reveals her true form as a transforming cat alien, revealing how she learned that the Star Color Princesses' power combined with Fuwa would unleash a great power that she wished to use to restore her people. Just then, however, the group finds themselves attacked by a vengeful Eyeone after she turns herself into a Notrigger. Seeing the Cures risking their own lives to protect her even after everything she had done, Blue Cat's desire to save them causes her to gain the power to become Cure Cosmo.

Realising that Eyeone is suffering as Darknest steals her consciousness, Hikaru retrieves the Aries Pen from Kappard but is still not powerful enough to defeat the Notrigger. However, Cure Cosmo is able to manifest the Rainbow Perfume and uses Aries' power to defeat the Notrigger and rescue Eyeone. After the Aries Star Princess is revived, Blue Cat, now going by her original name of Yuni, returns to Earth with the others to join their search for the Princess Star Color Pens. Meanwhile, back in the Notraiders' base, Darknest partially revives.

On Tanabata, which also turns out to be Lala's birthday, Hikaru's father Yoichi returns home from his research on aliens and cryptids abroad. As the family prepares a barbecue party to celebrate all three occasions, Hikaru explains how she encouraged Yoichi to go overseas and pursue his dreams, much to the dismay of his father Harukichi, who felt he was just abandoning his family. Just then, Harukichi, who blames himself for not raising Yoichi properly, is turned into a Notray by Tenjou, but is saved by Yuni. Afterwards, Yoichi and Harukichi manage to patch things up with each other before celebrating Tanabata with their family.

After eating one of Yuni's matter cookies, Fuwa develops hiccups that cause her to spawn multiple copies of herself, which only disappear upon being fed. As the girls try to keep the copies from being noticed, Elena joins Yuni in chasing after the real Fuwa, assuring her that she doesn't have to take on the responsibility all by herself. Kappard then captures the real Fuwa and uses energy stolen from the copies to power up his weapon. Learning to rely on the help of her teammates, Yuni manages to rescue Fuwa and defeat Kappard, after which they find the shock of being captured has cured Fuwa of her hiccups.

As Madoka laments over winning a piano concert that she felt should've been won by someone else, the girls travel to Planet Icesnow and discover the Aquarius Princess Star Color Pen is being used by a snowman alien named Yukio as a spare nose. Learning that Yukio wants to make the ice girl Iruma smile, the girls show him the fun things that can be done with ice and snow. Although Madoka struggles to make Iruma smile with a musical performance on icicles, Yuni contributes her singing to the mix, leading Madoka to realise that she should have fun with her playing.

The girls bring Yuni along to a summer festival, where she finds herself hesitating to have fun. Catching up to her, Lala tells Yuni about the fun she has spending time with Hikaru and the others, but Yuni is reluctant to prioritise friendship over her mission. Yuni is then confronted by Tenjou, who uses a multiplying Notray to capture Yuni and use her as a hostage against the others. However, the Cures manages to work with Yuni to rescue her and defeat the Notray. Afterwards, as the girls watch the fireworks together, the rocket receives a transmission from Lala's brother, Lolo.

Learning from Lolo that there is a Princess Pen on Lala's home planet of Saman, the girls begin heading there but are unable to warp all the way due to Fuwa being too tired. Needing to rest for the night, Hikaru decides to hold a pajama party with everyone. While getting to learn about each other during the party, they discover an alien named Yanyan has snuck aboard. Kappard attempts to use Yanyan's anger to power his weapon, but the Cures manage to defeat him. With the rocket too damaged to warp, Yanyan offers to take the girls to her planet to repair it.

Arriving on Yanyan's home planet Pururun, the girls receive pearls from Yanyan allowing them to transform into mermaids and swim underwater. However, they are soon pursued by Eyeone, who swears vengeance against Yuni for deceiving her and attacks with a robot. Although Yuni is shaked up by Eyeone's words, Hikaru gives her the encouragement to beat her. The girls eventually arrive at the core of the planet, where they can get their rocket repaired.

Elena and Madoka are asked by Flare, a plasma alien and engineer, to pump bellows to power up his flames for the rocket repair, but their stamina is unable to hold out. Hearing about how Flare left his planet to go to Pururun, Elena and Madoka talk about how much they envy each other, leading them to reevaluate themselves. Kappard then shows up to attack Flare's factory, but Elena and Madoka manage to surpass their own limits to beat him back. Filled with renewed motivation, the two girls successfully help Flare repair the rocket, allowing the girls to continue onward to Saman.

The girls arrive on Planet Saman, a planet largely influenced by AI, and meet Lala's family, including her twin brother Lolo. As Lolo is commended by the Space Alliance for finding a Princess Star Color Pen, he states that the alliance is interested in working with the Precure. This leaves Lala conflicted about whether to give a proper report on what they've been doing, leading Madoka to sympaphise with her and ask her what she wants to do. Just then, Tenjou attempts to steal the Star Color Pen by turning the head scientist Kuku into a Notray. Although the Cures manage to defeat the Notray, Kuku assumes that Lala is trying to steal the pen, putting out a warrant for the arrest of her and her friends.

Taking advantage of the confusion, Eyeone hacks into Saman's Mother AI and takes control of all the AI devices on the planet to lure the Cures out and capture them. However, Lala's AI sacrifices itself to protect the girls with the rocket. Eyeone attempts to have Mother take over the rocket, but Lala's AI manages to connect its data with Mother to undo the hacking and release the Cures. Revealing her identity as a Precure to her family, Lala uses the pen Lolo found to beat back Tenjou and Eyeone and revive the Cancer Star Princess. Afterwards, Lala's AI manages to return with its personality intact before the girls make their way back to Earth, unaware that the Space Alliance is following them.

Catching up to the girls as they arrive back on Earth, Topper of the Space Alliance requests that the Precure join them, but the girls turn him down due to their personal obligations. Noticing Hikaru's Twinkle Book, Topper takes her to his ship to talk about his failings and ask her to join the alliance to help him bring light back to the galaxy.

The Star Princesses explain that the Cures must continue to help Fuwa grow in order to restore the universe. Garuouga once again shows up to try and capture Fuwa, revealing how he came to rely on Darknest's power after failing to save his own planet. Steadfast in their desire to protect Fuwa, the Cures use the new Shiny Twinkle Pen to call upon a new power to destroy Garuouga's bracelet, after which Darknest leaves a cryptic message about Fuwa being a vessel. Afterwards, the Star Princesses tell the girls that they must search for something known as Twinkle Imagination in order for Fuwa to reach her full power.

While the girls have heaps of work to do upon returning to school, Fuwa becomes impatient waiting for them to finish as she wants to search for Twinkle Imagination. Running off on her own after the others call her selfish, Fuwa runs into Kappard, who turns Hikaru's pet dog Yeti into a shield. As Hikaru tries to save Yeti, Fuwa manages to use her new warping ability to aid her, allowing the Cures to rescue Yeti.

The girls are greeted by a cactus alien named Saboro, who is believed to be an inspector from the Space Alliance. Finding that Saboro doesn't use speech, Elena communicates with them using their gestures and shows them around town. However, Saboro becomes upset after Elena shows them her flower shop, leaving Elena to believe that she offended them. Upon learning that this Saboro is actually just a visitor, Elena searches for Saboro, only to discover that Tenjou has turned him into a Notray.

Madoka, who is approaching the end of her term as student council president, nominates Hikaru as a candidate for the next president, with Sakurako running against her. As Hikaru pushes herself to act like Madoka to try and win votes, she finds a notebook dropped by Sakurako detailing the various ways she hopes to make school a safer and more relaxing place. Just then, Kappard targets Sakurako to power up his weapon. However, Hikaru's desire to understand Sakurako awakens a power inside her, allowing her to defeat Kappard. Afterwards, Hikaru relinquishes the election to Sakurako, believing she is better suited to be her own kind of president.

Learning that a mafia boss named Don Octo possesses a Rainbownian ring, Yuni once again takes on the guise of Blue Cat to try and steal it, much to others' chagrin. Sneaking into Don Octo's hideout and retrieving the ring, Yuni finds herself up against a newly appointed space police officer named Ann, only for both of them to be caught by Don Octo. Just as the girls rescue them the duo, Tenjou appears and turns Don Octo into a Notray. With the support of both Ann and the Cures, Yuni manages to defeat the Notray and uses her honesty to convince Don Octo to give her the ring.

Hikaru and Lala decide to participate with their class in the Halloween costume contest held in the commercial district of the city, disguised as UMA, which includes Elena and her family, Madoka and Yuni. Kappard, meanwhile, recalls his planet of origin that has now been destroyed and vent his frustration that he has lost it: the Pretty Cures, in order not to frighten the crowd and make them discover the existence of aliens, improvise a scene disguised as fighters and push the enemy away to confront him. The best Halloween costume contest is finally won by Hikaru and Lala's class, by Elena and her family, by Madoka and Yuni and, curiously, also by Kappard.

Finding no clue as to what and where the Twinkle Imagination might be, Pretty Cure decide to enlist the services of Yuni's old acquaintance who inspired her to infiltrate the Notraiders as Bakenyan: The famous fortune-teller Hakkenyan of planet Uranine. Yuni is rather hasty and wants to quickly find the Twinkle Imagination to restore Rainbow, with Hakkenyan advising her to observe what is around her. But Yuni gets attacked by Eyeone who traced the Princess Star Color Pen's signal to her location, realizing that her deception caused Eyeone to be exiled by the Notraiders and from ultimately the only home she ever knew.

Elena's teacher announces that the school will be holding an English Speaking Contest and that Elena has been chosen to represent the school. Tenjou decides to disguise herself as a guest teacher and use her cover of mentoring Elena to capture Fuwa. But Tenjou ends up recounting memories of her home world during her interactions with the Precure. Elena writes a speech about how Smiles can connect people, but Tenjou tries to get her to write one about her feeling alone, which brings up old memories for Elena.

Madoka's Father, Fuyuki, receives a picture of Lala during the last Notraider attack and confronts her at the spaceship. Although Hikaru and Elena defend her with the help of Abraham and Yuni, Fuyuki still doesn't believe them and vows to discover the truth. The next day at school, everyone begins behaving strangely towards Lala. Hikaru confronts the class and finds out from Sakurako that Fuyuki spoke to her about Lala being an alien and that several members of the class remember strange things happening whenever Lala was around.