Fourth grader Aoyama and a mysterious older woman known to him as Onee-san (Lady), who is a dental assistant and also Aoyama's first crush, seek out to discover the reason why penguins are suddenly appearing in Aoyama's quiet suburban neighborhood.
Tropes in this work include:
- Adaptational Alternate Ending: Downplayed, the novel leaves it very deliberately unclear whether Onee-san would ever return. The anime adds an extra scene for its very end where Aoyama's Lego Penguin plane was returned to him by a penguin after an unknown amount of time, suggesting that she's still capable of interacting with Earth, wherever she is.
- Adaptation Explanation Extrication: Uchida brings up the fact that he finished surveying the river and discovered that it's an inexplicable loop with no source in the anime, but it's just brought up as another weird thing on their plates and given little thought after. The novel explains that it was a side effect of the Ocean's presence and after it's fixed by the penguins, the river reverts to being normal with parts of the loop just completely drying up.
- Adorably Precocious Child: Aoyama and Hamamoto. Aoyama observes and catalogs everything that catches his interest, making notes and drawing charts of his experiments. This ranges from the penguins, the Ocean, his baby tooth that fell out and Onee-san's breasts. Meanwhile, Hamamoto is introduced holding a book on the theory of relativity and is very good at chess. They both seem to get it from their fathers, both of whom are prominent researchers in their respective fields.
- Alice Allusion: Jabberwocky is mentioned by Onee-san, who says that the illustration of the Jabberwock gave her nightmares. It relates to the seemingly-nonsensical nature of the penguins and Ocean. During the climax, when inside the Ocean, buildings and landscapes warp and connect together in bizarre ways, much like falling down the rabbit hole.Alice: It seems very pretty, but it's rather hard to understand! Somehow it seems to fill my head with ideas - only I don't exactly know what they are!
- All Love Is Unrequited: Many of the romantic interests in the story are one-sided such as Suzuki's for Hamamato and Hamamato's for Aoyoma. Zig-zagged with Aoyoma and Onee-san's case; while she doesn't have the same romantic feelings for Aoyama that he has for her, she cares for him deeply.
- Ambiguously Human: Onee-San can turn objects into penguins, doesn't need to eat, and sickens if she gets too far from the Ocean. She has memories of living a normal life, but wonders near the end if they really happened.
- Artistic License – Ornithology: Not in Japanese or English, but in French due to a gross mistranslation. The French word "pingouin" normally means "razorbill", a sea bird living in the Northern Atlantic. However, the translation treats it as an equivalent of "penguin", whose actual French translation is "manchot". Thus during the whole movie you get gems like "razorbills live in Antartica" or "the Adélie razorbill". It is likely that since the confusion is frequent among French speakers anyway, the marketing department opted for the cuter word rather than an accurate translation.
- Bitch Slap: Hamamoto delivers an impressive one to Suzuki, when he coughs up the secret about the Ocean to the researchers.
- Book Ends: The story starts and ends with Aoyama narrating his intentions as he does his morning routine.
- Brutal Honesty: Aoyama admitting that he knows Suzuki is bullying him due to the latter's crush on Hamamoto and denies any "lovey-dovey" is going on...while the other two are right there. He then advises Suzuki to be more logical in admitting his feelings.
- The Bully: Suzuki, with his two cronies parroting almost everything he says. They torment several kids in the class, although they seem to focus on Aoyama and Uchida. Uchida, being rather shy and nervous, is afraid of them; Aoyama, on the other hand, barely reacts to their taunts and doesn't hesitate to confront Suzuki.
- Buxom Beauty Standard: Aoyama certainly thinks bigger breasts are more attractive.Hamamoto: You only like [Onee-san] because she has boobs!
Aoyama: Yes, but the way I like her is separate from that.
Hamamoto: But you still like boobs!
Aoyama: Yes. Large ones. - Cessation of Existence: It's left ambiguous exactly what happens to Onee-san once the Ocean is destroyed. It's true that she no longer exists in the "real world" but whether or not she and the penguins still exist in some capacity on the other side of the Ocean is unclear, although the penguin that appears at the very end to return the Lego plane suggests she is alive.
- Clingy Jealous Girl: Hamamoto is immediately at odds with Onee-san the moment the two meet. Even at the prospect the penguin highway is connected with the Ocean, she refuses to work with Onee-san because she wants Aoyama's attention.
- Crush Blush: Suzuki around Hamamoto. Hamamoto also blushes once or twice around Aoyama.
- Daddy's Girl: Hamamoto and her father are shown to be very close. Her own academic inclinations seem to be modeled after him. When he disappears into the Ocean, she's absolutely despondent.
- DIY Dentistry: Zigzagged. Onee-san is a dental assistant but offers a home remedy for Aoyama's loose tooth. Played for laughs in that every time she moves, Aoyama follows her, defeating the whole purpose.
- Eating Optional: The penguins don't need to eat. Neither does Onee-san.
- "Eureka!" Moment: Discussed between Aoyama and his father when Aoyama is talking about the difficulties he's having putting everything together in his research. Later, Aoyama has one when the connection clicks.
- Gang of Bullies: Suzuki and his two unnamed cronies, who consistently hound Aoyama (due to the Love Triangle) and his friend. They're also shown messing with the other boys in class.
- Good Parents: Aoyama's father is nothing but supportive of his son's exploits and gives him the means to continue his research. Aoyama's mother is also one in terms of looking out for Aoyama's health.
- Groin Attack: When ambushed by Suzuki and cohorts, Aoyama squeezes Suzuki between the legs to make a getaway. Suzuki returns the favor when he catches Aoyama. Near the end of the film, Suzuki does the same move on one of the evacuation crew so that Aoyama can run to find Onee-san.
- Heroic Sacrifice: Onee-san destroys the Ocean even though she may not be able to survive at the end. She disappears after, her ultimate fate unknown.
- Intergenerational Friendship: Aoyama and Onee-san; he's a fourth-grader and she appears to be in her 20s.
- Jerk with a Heart of Gold: Suzuki is an arrogant bully who takes pleasure in picking on Aoyama. He shows his good side during the climax when he helps Aoyama escape the school to find Onee-San.
- Kryptonite Factor: Aoyama and Uchida, while trying to transport a penguin, are distressed when it begins to show signs of sickness, eventually turning back into the soda can it started out as. Onee-san shows the same signs as she and Aoyama are trying to take a trip to the beach, hinting that the further she gets from the Ocean, the worse she feels.
- Love Triangle: Aoyama has a crush on Onee-san while Hamamoto has a crush on him and Suzuki has a crush on her.
- Magic Skirt: When she gets caught by one of the evacuation crew, Hamamoto gets held under one arm. Despite all her struggling, hitting and kicking, her skirt remains in place. However, this means nothing if you're standing behind her, like Suzuki, who suffers a minor freak-out before pulling himself together.
- Mind Screw: During the climax, when reality is unraveling due to the Ocean expanding. Geography makes no sense, buildings and objects float in the sky, the world wraps around itself, paths lead to where they logically shouldn't and so on. And that's not getting into the whole symbolism around the theory of Relativity and what Onee-san, the penguins and the Ocean are.
- Misplaced Wildlife: Penguins obviously don't naturally live anywhere near the suburbs, much less anywhere in Japan. Aoyama wants to figure out where these penguins are coming from.
- Modesty Towel: Played with. After Onee-san and Aoyama eat in her apartment, she flops over and falls asleep. He draws her in his research notebook, then sees that her shirt has pulled up some and drapes a towel over her belly.
- My Eyes Are Up Here: A reverse variant when Onee-san notices Aoyama's eyes wandering up from the chess board a bit too often.
- Nice Girl: Onee-San is very cheerful and friendly, and treats Aoyama almost like he were her son.
- No Name Given: The dental assistant is only named Onee-san all throughout (Lady in the novel).
- Not So Stoic: Aoyama has his moments. Besides being somewhat obsessed with large breasts, he occasionally drops his facade, especially when under stress.
- Pants-Pulling Prank: Suzuki and his lackeys pull Aoyama's swim trunks off while the class is in the pool. Aoyama, without missing a beat, calmly gets out of the pool in front of all his classmates and walks up to Suzuki as everyone else recoils.
- Pot Calling The Kettle Black: During Suzuki's introduction, Aoyama calls him arrogant. This is right after Aoyama's self-introduction describing how smart, amazing and popular he is/will be.
- Power Incontinence: Onee-san doesn't know how or why she makes the penguins, it just happens. Aoyama's research is to explain her powers better. Though she might have just been pretending to not know to give Aoyama a mystery to solve. Alternatively, her memories were locked away until The Reveal. She also unconsciously creates monsters based on the Jabberwocky illustration, out of her desire to continue existing.
- Precocious Crush: Aoyama, a fourth-grader, has a crush on Onee-san, an adult. This is much to the dismay of Hamamoto, who has a crush on him while he's fixated on an adult woman she can't possibly compete against.
- Reality Bleed: It's revealed in the end that the Ocean's mere presence edited reality to make the clearing behind the forest for it to be present in and the looping river around town. Once the penguins fix it, both disappear from reality.
- Shout-Out: The function and appearance of the Ocean is similar to the titular alien ocean in Solaris. Like Solaris, it can alter physical laws and create living things with false memories that disappear if removed from its influence, and its purpose (if any) is totally incomprehensible. Stanisław Lem is also referenced for a gag when Aoyama makes up a fake disease named after him to scare Suzuki at the dentist.
- Smart People Play Chess: Played straight by Hamamoto; she's the best in the class by far. Somewhat downplayed by Aoyama who is pretty good but is being taught by Onee-san, who seems to be more of an average person than a genius like either of the two kids.
- The Stoic: Aoyama is pretty unflappable and straightforward, even in times when other kids would be horribly embarrassed or angry, although there are times when he's obviously holding himself back from emoting.
- Sugar-and-Ice Personality: Aoyama is largely stoic and emotionless, but is shown to deeply care for his loved ones. He's protective of Onee-San and comforts his sister when she learns about death.
- They Would Cut You Up: Aoyama's major concern on keeping the origin of the penguins a secret is to protect Onee-san from becoming a test subject. He's very firm about that, whether or not that would actually happen.
- We All Die Someday: Aoyama's sister comes into his room freaking out because she's realized that their mother is going to die. Aoyama calmly explains that death comes to everyone, and comforts her as she cries.
- Where the Hell Is Springfield?: It's deliberately vague where the story takes place, with the only major identifiers being that it's landlocked as Aoyama makes a promise with Onee-san to see the coast for the first time with her and there's a local university with a meteorology lab.
- You Were Trying Too Hard: Despite "Eureka!" Moment being discussed by Aoyama and his father and him even writing it down, Aoyama fails to take his father's advice and ends up working to the point of sickness. It isn't until after he's recovered and stopped concentrating on his work that all the pieces start to click together.
