Angered by the pollution in the seas, a squid girl named Ika Musume comes from the sea and declares the invasion of Earth at a nearby yakisoba stand, but isn't taken seriously due to her small stature. When she goes to plead her case, she is mistaken for a waitress, which puts the responsibility of invading the world into perspective. When she breaks a hole in the store with her tentacles trying to hit a mosquito, the store manager, Eiko Aizawa, puts her to work in order to pay for the damages. Later, Ika meets Eiko's little brother, Takeru, who goes to great lengths to pretend to be a squid-person so he can be Ika's comrade. During a rainy day where there are few customers, Ika takes the opportunity to try and take over the stand, but is overpowered by the eldest sister, Chizuru. As punishment, Ika is forced to use her own ink to make Squid Ink Spaghetti, which becomes popular.

Ika meets lifesaver, Gorō Arashiyama, though gets annoyed when he doesn't live up to her definition of 'protector of the sea'. Ika tries to drown him to show him up, but this in turn prevents him from reaching a kid trapped in a current, so Ika must save her herself. After witnessing a birthday party, Ika decides she wants one as well, so the Aizawa sisters hold a party for her before playing with some fireworks. Ika later meets Aiko's friend Sanae Nagatsuki, who takes a creepy liking towards her and forces her to cosplay for her personal photo collection.

The gang take Ika, who had never heard of ghosts before, on a test of courage at the local cemetery, but she just ends up scaring everyone with her ability to emit light. Later, Ika becomes frightened when inflatable killer whales start showing up around the place (believing they are real), since killer whales are her natural predator. When Takeru asks Gorō to teach him how to swim, Ika tries to teach him to avoid the whales. Later, a new girl, Nagisa Saitō, joins the stand, though is a bit nervous around Ika, who becomes pleased that someone actually fears her.

When Ika finds a lost wallet, the owner rewards her with 10,000 yen, which she spends on frozen shrimp. When the TV in the beach house breaks down, Ika is invited to sleep over at the Aizawa household. While exploring the beach, Ika and Eiko find an imitation Squid Girl built by the owner of a rival beach house, Southern Winds, to attract customers. The owner challenges Eiko to various matches for possession of the original, though the imitation's efforts prove scary.

A woman named Cindy Campbell who comes from a US extraterrestrial research laboratory believes Ika to be an alien and wants to take her back to her lab. Cindy attempts to brainwash Ika into thinking she's an alien, but her appetite snaps her out of it. Later, Ika has a look around Eiko's school, believing it to be a military base. She decides to hold the principal captive and take over the school before Eiko stops her. Later, Sanae has a dream in which Eiko finds a miniaturized Ika and keeps it as a pet.

A hero show is performed on the beach for the kids, though the performers run into a bit of trouble when Ika somehow manages to get everyone to cheer for the villain. When Ika then takes the costume for herself, Chizuru acts as a guest character to set her straight. Later, Eiko is shocked to find Ika is able to solve complex math problems. She reluctantly asks her to teach her how to study, only to find the technique is illegible to humans. After Gorō rescues her from drowning, Nagisa becomes concerned that he may have been brainwashed into thinking Ika isn't a threat, leading to some strange misunderstandings.

Concerned about any evil plans Ika may have, Nagisa decides to sleep over at the Aizawas to keep watch on her. Nagisa pretends to not be scared of Ika, which upsets her. Eiko tries to convince Ika to just be friends with Nagisa, but Nagisa's fear rises up again. As Ika decides to play as being Queen, Cindy manages to trick her into agreeing to come to her secret laboratory, where she meets some her strange co-workers; Harris, Clark and Martin. Later, the girls run into the Southern Winds owner's daughter, and offer her a trial run working at the Lemon. As she attracts more sales, Eiko lets the owner have Ika for the Southern Winds, where she proves to be a worthwhile entertainer.

Ika gets a fever, which she believes to be a special Squidgirl disease revolving around a craving for shrimp, so Eiko tries to help her stay off shrimp until she gets better. Later, Ika learns about the fins on her hat and everyone tries to figure out what they are used for. She also gets into a debate with one of Takeru's friends over sandcastles. Later, Ika becomes fascinated by umbrellas believing them to be ideal weapons.

While trying to avoid Chizuru's wrath after a failed attempt at doorbell ditching, Ika ends up making friends with a schoolgirl named Kiyomi Sakura. Ika invites Kiyomi over to the Aizawa household, but becomes paranoid that she'll get punished for not asking permission. Later, Ika tries on lipstick for the first time and becomes interested in all sorts of makeup. After that, Sanae and Cindy get into a fight over their respective desires for Ika. Later, the MIT trio bring over a special device which turns out to be a disintegrator ray which destroys the whole beach house.

On a rainy day, Ika exhibits a talent for art, though the depictions of her friends are somewhat scary. Later, Eiko tells Sanae that she should give up on her crush on Ika and try to become proper friends with her. However, holding herself back from Ika proves to be harder than Sanae thought. Later, when Kiyomi's baseball team falls short one member, Ika decides to help her out. Though she initially has trouble with the game, her tentacles soon come into good use.

Eiko finds an old doll from her childhood that freaks Ika out as it appears to move by itself overnight. As Eiko recalls the doll's features, she and Sanae wonder about the whereabouts of the other doll in the set. Having witnessed her abilities first, Cindy starts to wonder if Chizuru is actually an alien and elists the help of the MIT trio to gather some DNA. Later, Ika and the Aizawas go on a hiking trip to the mountains, where Ika's tentacles seem to attract the appetites of the wildlife.

A beach volleyball tournament is held with a 3D television as top prize and Ika and Eiko decide to team up, managing to reach the finals against Gorō's team. When Eiko twists her ankle during the match point, Chizuru takes her place and wins the competition. Later, Ika's tentacles suddenly stop working, along with her other squid abilities, and the others try various methods to bring them back with no avail. Although the others suggest it would be alright if Ika returns to the sea, everyone becomes lonely when Ika doesn't immediately return. Ika later returns with her tentacles cut off, residing herself to being a normal girl, though Takeru makes it clear this isn't what makes her happy. As Ika laments on the beach, she meets a girl named Kozue Tanabe, who assures her not all humans are bad and that she is not alone. As Ika and Eiko go swimming in the sea, they are caught in a whirlpool caused by the MIT trio, and Ika's desire to save Eiko causes her tentacles to grow back, allowing her to rescue Eiko from drowning.