Amane Fujimiya is a socially awkward first-year high school student who lives by himself in an apartment. His neighbor is schoolmate Mahiru Shiina, a girl who is so beautiful and so unreachable that the other students call her an "angel." On the way home one day, Amane notices Mahiru sitting alone on a park swing, drenched in the rain, so he lends her his umbrella. When Amane catches a cold the next day, Mahiru insists on taking care of him, and the two next-door strangers embark on an unusual new relationship.

On the way home from school, Amane finds Mahiru stuck with a sprained foot after rescuing a cat in a tree. He performs first aid and then carries her home. The next day, Mahiru brings Amane a container of food as thanks, and Amane accidentally blurts out something he has been thinking: "I'd love to eat it freshly made sometime." As a result, the two agree on conditions that will allow them to share fresh-cooked dinners in Amane's apartment. When Amane stuffs his face while praising Mahiru's "delicious" cooking, it isn't hard to imagine the two as a newlywed couple...

Amane's mother, Shihoko, arrives at the apartment without warning while Mahiru is visiting. Amane asks Mahiru to hide, but Shihoko eventually finds her, and the two neighbors frantically try to correct Shihoko's assumption that they are dating. Nonetheless, Mahiru is touched by Shihoko's motherly kindness. After Amane sees how happy Mahiru is to be called by her first name, he tries calling her "Mahiru" too. From that day on, the neighbors call each other by their first names.

When Itsuki and Chitose visit Amane's apartment for a Christmas party only to discover that the angel Mahiru lives next door, they instantly become very curious about the relationship. Chitose, obsessed with cuteness, insists on becoming friends with Mahiru. The day after Christmas, Amane notices that Mahiru has a fever. Despite Mahiru's stubbornness, Amane convinces her to stay and rest in his room. When Mahiru sees Amane so diligently taking care of her as if returning the favor she did for him that one memorable day, it seems to put her at ease.

Mahiru and Amane ring in the new year together. When the exhaustion from cooking catches up with Mahiru and she falls asleep in Amane's arms, Amane has no choice but to let her stay the night in his bed. The sight of her sleeping peacefully but totally unguarded gives him a bit of a jolt. Two days later, Amane's parents come to visit. When the four go to Hatsumode (the first shrine visit of the year), Amane is taken aback by how pretty Mahiru looks in a kimono. Meanwhile, Mahiru keeps blushing at the sight of Amane dressed up so handsomely.

On Valentine's Day, after the two neighbors eat dinner together as usual, Mahiru gives Amane some hot chocolate. Amane accepts it as a normal Valentine's Day gift, but Mahiru seems restless, as if she has something to tell him. When Mahiru rushes home, still unable to say what's on her mind, Amane notices a small bag with a card at his front door. Inside the bag are chocolates that Mahiru made especially for Amane, who had said that he doesn't like very sweet things. In return, Amane gives Mahiru a special present on White Day.

The day before spring break, Itsuki has a fight with his father and asks Amane to let him stay over. When Chitose finds out that her boyfriend will get to enjoy Mahiru's cooking, she demands to join them and stay at Mahiru's apartment. The four friends spend the next few lively days together. After Itsuki and Chitose leave, Amane returns home one day to find Mahiru confronted by her mother, Sayo. Noticing Mahiru's dark expression and sensing that something is wrong, Amane invites Mahiru in. The two sit together on Amane's sofa as Mahiru timidly explains her complicated history with her parents.

When the new school term starts, Amane and Mahiru are put in the same class. At home, Amane makes meal requests and gives Mahiru gifts. The two neighbors' relationship is almost as intimate as if they were married. At school, however, Amane treats Mahiru like a stranger. When Mahiru notices how differently Amane treats Itsuki and Chitose, she gets the uncomfortable feeling that she is being left out. Mahiru tries to think of a way to gradually get closer to Amane.

"Amane-kun, I want to go shopping with you during Golden week." Amane accepts Mahiru's invitation and the two get dressed up to go out on a secret date. The neighbors talk, hold hands, and fully enjoy their special day out on the town. When stopping for a break, they coincidentally bump into Yuta, who quickly puts two and two together. The next day, Itsuki and Yuta grill their buddy Amane about whether or not he has feelings for Mahiru. Amane starts to feel the pressure from his friends' sharp questions.

Amane explains the reason he left home in middle school and began living alone. Mahiru empathizes with his sorrow and embraces him. "At least let me spoil you a little." The next day, Mahiru's classmates ask her about the boy she was seen walking with. Mahiru nonchalantly admits that it was a date, surprising Amane. Mahiru then confesses, "there's no one more dear to me in life than him."

Amane's studying pays off and he reaches sixth place with his midterm exam scores. Mahiru had promised to do anything he asked if he reached the top ten, and Amane somewhat reluctantly ends up laying in her lap again. Mahiru smiles at Amane as he eventually gives in and falls asleep at her hands. Not long after, Mahiru also falls asleep. When Amane wakes up and has to carry the half-asleep Mahiru back to her own room, she unwittingly invites him to sleep next to her in bed.