The story begins with the eldest sister Iina appraising the red library uniform designated for her baby sister Kokoro who is starting out as a librarian at Kokoro Library. After the middle sister Aruto scolds Kokoro to always be punctual and Iina photographs the occasion, Iina and Aruto's divergent perspective of professional conduct gives way to the three sisters opening the library only to encounter little action until the lunch break where Kokoro is advised to be patient -- very sage counsel when her first customer Kaede Hoshino arrives searching for an out-of-print book that Kokoro successfully locates on her own. After a calendar week, Kokoro ironically finds that Kaede Hoshino's failure to return the borrowed book in person causes her hefty heartache that leads to a collaborative hitchhiking sequence that proves Kokoro's ability to travel safely by herself but is otherwise in vain; during the drive home, Iina and Aruto exchanging notes about having to be strict becomes the preamble for Kokoro having forgotten that she only had to check the mail at home before undertaking the journey she did.
Kokoro's expository discourse about the hobbies and special skills of her elder sisters along with her own gives way to Jun Uezawa arriving at the Library to deliver some books; a »Take it and leave me alone!!!« toss of the approval stamp at her from the sleeping Aruto later, Kokoro races out to approve the delivery but forgets to bring the cart with her. After some small talk and Aruto imparting her stamp of approval unto Jun as an admonition to watch his words, the books being successfully unloaded gives way to adding them into the computer database and stocking them on the shelves after adding the Library label to them. Aruto is concerned about the meager traffic the Library sees and gets into a divergent concourse with Iina over the best method to attract more commerce; according to Kokoro, the problem is not what the Library has but that it is not community discourse. As Jun sets course for town with the newly created flyers, Aruto accidentally hurts Kokoro's feelings with her pragmatism; the thing is that Iina and Aruto only had to wait for Kokoro to return to the Library and for enough time to pass for everybody in town to swarm the Library en masse.
Kokoro and Iina's prior knowledge of Aruto's uncanny intuition about the logistics of catching forty winks after a nocturnal composition session does very little to prepare them for the half-asleep Aruto to French-kiss them when they solicit her assistance; while Kokoro and Iina are comparing notes about their love lives, Aruto wondering how they can have a boyfriend when they live in a remote library in the mountains sets the stage for Kokoro to hold up a Kirin Himemiya novel and generally muse about the mechanics of romance oblivious to the fact that Aruto and Kirin Himemiya are one and the same person. Later that night, Aruto finds that the mirage is more trouble to maintain than it is worth; if the half-asleep Kokoro wandering in on her looking for the toilet and the fast approaching deadline is not enough, her editor Sarara Saeki has set up an author's interview with Kokoro and plans to pick up the manuscript of the novel. Her protests falling on deaf ears, Aruto has no choice but to prosecute the interview in which she almost gives herself away; after Aruto explains the rationale behind the subterfuge, Sarara finally decides against blowing the whistle if Aruto successfully composes another title in a month's time.
Iina and Aruto exhibiting their swimsuits gives way to a divergent concourse over whether Kokoro should be cute or cool extinguished by the arrival of a thunderstorm that threatens to make their vacation plans a moot point; fortunately, the storm blows over and the three sisters are on their way with poor Jun none too pleased to be stuck house-sitting the Library. Aruto inquires Iina the logistics of lodging during the vacation; while there is no financial cost per se, Aruto is not thrilled to have it explained that she has to do librarian work on her vacation and makes a break for the beach when Iina charges Kokoro a delivery -- a delivery to a housebound girl named Misato Fukami that wishes proximity with a dolphin. While Aruto's subterfuge backfires on her, Akaha explains Misato's prologue to Kokoro who decides upon a euphoric epilogue as she races home. Unfortunately, Kokoro's decision the next morning to lead the two cousins over to the cape where the dolphins are ignites a firestorm within Misato's family government along with her own for which Jun pays dearly; the silver lining is that Misato gets her wish twice over, while Kokoro learns that a good librarian makes her customers happy.
Iina humming the opening theme as she brushes her hair prior to retiring for the night shows her zeal for photography whose subject of choice is her baby sister Kokoro -- a stewardship reaffirmed alongside Aruto. As if she sensed Iina's vow, Kokoro awakens to spot a hot-air balloon -- and a crime challenge at the door the next morning; Aruto's divergent concourse with Iina making sport of the challenge gives way to Inspector Kajihara arriving with a bunch of female officers to besiege the building and mistakenly arrest Jun who was worried about the girls' safety. Unfortunately, the Funny Tortoise Thief is not daunted as he prosecutes a sequence of disguises and wields the circumstances to his advantage when Kokoro's pet cat kicks the locked book out the window in a panic as it glares at the policewoman who caught it with a hissing growl. Even though Kokoro reasons that he has not yet accomplished his objective and Aruto smells a rat, the Thief is no doubt biding his time and hiding in plain sight for when the time is right; if Kokoro lending out the locked book (aka her father's diary) to the Thief as if it were a library book is not enough, the truth is that the Thief was directed by the girls' father to steal the book while checking in on them, and the Inspector only had to wait a week to catch the Thief.
Akaha complimenting Kokoro on a job well-done in checking out a book she wants gives way to having it explained that Kokoro is set to attend a librarian training course the next day in another town. While seeing off Kokoro, Iina cannot help but to impart some motherly counsel to her beloved baby sister as the train is preparing to depart while Aruto has complete faith in Kokoro who encounters a lady on the train that keeps her company to encourage her. Registration successfully being conquered does nothing to prepare Kokoro for coming face to face with the comparoid June nor for having it explained that Hibiki Asakura is to lead her through a different training regimen than the other students. Unfortunately for Kokoro, the technique to pass the test is to emphasize expeditious clerical work rather than quality customer service; even with June doing the referencing while she checks books in and out, Kokoro taking to the streets to retrieve an overdue book has the consequence of June following suit and there ultimately being no change in her professional status.
Aruto relaxing in the hot tub before Kokoro joins her makes for a very awkward scene for the co-dependent and overprotective Iina to encounter, especially since Kokoro is planning to attend a librarian training course in another town the next day. While seeing off Kokoro, Iina cannot help but to impart some motherly counsel to her beloved baby sister as the train is preparing to depart; unfortunately for Aruto, Iina doing a poor job of coping with Kokoro's absence means that she is effectively running the whole library by herself even when Iina decides to instead follow her around while prosecuting divergent speculation as to why they have not heard from Kokoro. Jun Uezawa makes poorly timed jokes inflame Iina's worries during a delivery leading to Iina getting angry with him. Iina's spirits pick up when Kokoro calls that evening; in spite of Iina's unrealistic nightmare disrupting Aruto's nocturnal composition. Iina ultimately finds relief in a temporary Kokoro replacement when Akaha comes to keep her company for the day, per Kokoro's request. A journal detailing her parents' prologue when Kokoro Library was built renews her resolve when Kokoro returns with no change in her status because she was helping a customer.
Kokoro has no time to ponder her professional purgatory when she finds herself the mentor to a taciturn girl named Hikari Inoue bearing a Librarian Association commission as a special-case librarian just like herself. While Iina and Aruto speculate on Hikari's perspective of her new surroundings, Kokoro takes it upon herself to warmly welcome her protege with some brewed tea; even with a custom-designed librarian uniform demonstrating Iina's goodwill, Hikari is too wracked with anxiety over her mom's medical status to acknowledge that labor is expected of her at Kokoro Library. Considering the significant headway she makes with the daily chores at the Library and even accommodating Akaha borrowing a book under Kokoro's tutelage, it seems that Hikari just needs somebody to pay attention to her and spend time with her. While watering the flowers, Kokoro's notice of a photograph of Hikari's mother prompts a »Hands off the photo, sister!!!« repulsion from the fleeing Hikari; a nocturnal foot race later, Hikari's confession about wanting to see her mother leads to Hikari finding a kindred spirit in Kokoro who was never given the choice to meet her mother.
An uneventful morning of holding down the fort at the Library sets the stage for Kokoro to have demonstrated that Hikari's cynical personality is very similar to that of Aruto as a child when she questions such things as why Kokoro Library was built where it is and bluntly defines the weaknesses of a Kirin Himemiya novel. Her mother Akari in tranquil waters, Hikari takes very well to Kokoro as the two girls head off to take a bath together before bed much to Iina's anguish. Unfortunately, the headway catalyzed by Kokoro's guidance quickly evaporates the next morning when Hikari learns that Akari is to undergo surgery -- a very difficult procedure that could cost Akari her life in fair weather. Crestfallen that Hikari could end up an orphan like herself along with her elder sisters, Kokoro rushing outside to cry out for her parents' intercession with Iina and Aruto right on her heels secures Akari's survival and prompts Hikari to secretly steal away at dawn much to Kokoro's anguish; Iina recklessly driving her amphibious automobile; Kokoro arriving at the station to a very sentimental scene of Kokoro reminiscing about the good times after handing Hikari all the photos Iina took of their time together which prompts Hikari to acknowledge her human fallibility as the train accelerates.
Akaha arriving for a visit one afternoon to explain to Kokoro about the inauguration party for the mayor Marie Momochi she attended with her mother Midori, tells the sisters of the Mayor's intention for a weekend visit. While Akaha and Kokoro speculate that the Mayor is inviting them to a party, Aruto and Iina suspect that it is for a far more sinister reason but support Kokoro's decision to welcome Marie with a sign the next morning only to find that Marie has a hostile political volition. Iina is surprisingly pragmatic about the whole situation later that evening as she defeats Kokoro's advertising proposal by stating the logistical obstacles of arriving at Kokoro Library. Iina and Aruto do not have to observe their sibling for very long to realize that Kokoro's anguish would eventually get the better of her. Aruto offering to write more novels as an income engine for the library becomes the preamble for Iina to again exhibit her insight regarding the big picture. Kokoro overhears her sisters' divergent concourse and races off to locate her father's diary that she hopes will save the Library.
Upon overhearing Iina's conversation about it with Aruto, Kokoro patiently bides her time and is rewarded with the opportunity to read her father's diary which starts out detailing the calm before the storm before her father Joldy Sun is jolted out of denial about the presence of the war. Meanwhile, a nurse named Kokoro Shindou heading over to the library seeking another book for a young girl named Akari Inoue sets the stage for Joldy to arrive on the scene and see for himself that the city is in a bad way; on December 11, the commanding officer has it explained to him that the enemy has gathered in the nearby city of Ektar and that an invasion is not out of the question. The android July points out the route the enemy is likely to avail in its advance and suggests setting up a choke point; after 13 days of uneventful observation, the enemy making its move leading to July offering her power source to detonate the explosive charges rigged to the bridge. The two countries now at peace, Joldy decides to build his life in the town when Kokoro approaches him accompanied by the townspeople who wish to return the books he lent them which are of quantity requiring far more than a cabin to house, hence the advent of Kokoro Library.
Upon reading her father's written account of why Kokoro Library was built, Kokoro firmly resolves to continue running Kokoro Library alongside Aruto and Iina for as long as she can even though she tells Akaha that she can be a librarian pretty much anywhere. Kokoro bursts into tears, the Funny Turtle Thief explains that crying her eyes out will not solve anything and to reflect upon the sentiments that she has felt during her prologue as a librarian for clues as to what has to be done. Kokoro decides to share her father's prologue behind Kokoro Library as she sets course for the city only to find that her sisters feel the same way and that the logistics of the journey are easier said than done. Iina's car malfunctioning, Jun's car exhausting its fuel supply, and Kokoro's motorcyclist friends being stopped in their tracks by a landslide . . . the Funny Turtle Thief becomes the key to a vital journey to Mayor Marie Momochi who explains that the people have made it crystal clear that it will cost her her seat as mayor if she insists on closing Kokoro Library. In the months ahead, Kokoro Library develops a home delivery/retrieval service for its library books.
Iina and Kokoro set out on Christmas Eve with the reluctant Aruto to the city in order to hand out good cheer to the people there that may not know of Kokoro Library. On Christmas Day, Akaha decides to spend the night with Kokoro excited about all the girl time they will get to spend together alongside Iina and Aruto when a blizzard nearly buries the Library the next morning. Everybody cuddling together to share body heat after the kerosene is depleted and the girls' attempt to entreat the assistance from the Tortoise Thief fails. Kokoro reflects upon her initial encounter with Akaha who became lost in the forest while chasing a squirrel; an escort journey later, Kokoro has two new friends and customers for the Library. The Thief defrosting the Library and affording a successful rescue gives way to Kokoro developing a winter illness the next day that forces Iina and Aruto to divide their energies in nursing Kokoro back to health and operating the Library; after Aruto ends up taking Kokoro's ailment unto herself, the fully recovered Kokoro remarks that the cold winters the Library experiences in the mountains are no match for the mutual love she has for her sisters.