The sea in our world has been polluted. All sorts of trash were thrown into the sea, making it unpleasant deep under the sea. One of the inhabitants of the sea, Ika Musume (Squid Girl) seeks to exact revenge on humanity for throwing trash into the sea. Clueless about the surface, she seeks to invade humanity alone, trying to rule over the world, only to find herself slaving away at one of the nearest beach-houses for breaking a side of its wall.
After renewing her resolve to invade mankind, Squid Girl suspects various things to be counter measures against her. Later, Kiyomi and her friends come to the Lemon to see Squid Girl, much to the dismay of a very jealous Sanae. When the sea becomes filled with jellyfish, the Lemon holds a contest to see who can catch the most jellyfish.
Squid Girl joins Takeru to elementary school, where the teacher becomes jealous of her popularity. When some bullies take over the playground, Squid Girl challenges them to a game of soccer, which proves tricky without her tentacles. Later, Eiko tries dressing up Nagisa as a guy to attract female customers, which also stops Squid Girl's teasing. Ayumi also comes to work again, being dressed in a maid's outfit equipped with a metal knuckle to overcome her shyness. However, they both stop after Ayumi's father points out this isn't solving the core issues. Later, Eiko and Chizuru are surprised to find Squid Girl has the ability to change her weight at will, leading to some odd experiments.
Noticing Sanae's dog, Alex, being jealous of Sanae constantly giving Squid Girl attention, Eiko suggests Squid Girl take him for a walk so they can bond. Though they don't initially get along, they help each other out when they are attacked by a ferocious dog. Later, Squid Girl observes some kids doing morning exercises and can't get them out of her head, leading to some trouble at work. Afterwards, Goro puts Squid Girl to work as a lifesaver, but after a couple of false starts, Goro doesn't trust her when she actually notices something dangerous in the water. However, after she manages to save some drowning kids, Goro understands that she protects the sea in her own way.
After Takeru has trouble understanding a tourist, Cindy holds an English-teaching session, with Eiko being the only one who doesn't understand anything. This leads to some communication errors as Cindy misinterprets Eiko's Japanese as English. Later, Squid Girl learns about tickling from Eiko and starts going around tickling others. However, she gets her comeuppance when she attempts to tickle Chizuru and ends up catching hiccups, which she believes can only be cured if something makes her happy. Later, Squid Girl joins Takeru and the others by the river, where they have a race with grass boats. As Squid Girl follows her boat down the river, she winds up on a completely different beach.
When Takeru buys a remote-controlled car, Squid Girl takes it outside for a drive, but ends up breaking it. Feeling guilty, she offers to be a replacement herself, but soon apologises for breaking it. Later, everyone writes down their wishes for Tanabata, with Squid Girl struggling to narrow her choices down to one wish. After Takeru finishes his summer homework, Squid Girl tries to help him find ways to play by himself.
Goro accompanies Chizuru on a lengthy jog whilst Eiko and Takeru take Squid Girl on a tour of the city, where she becomes shocked at the sight of a large Buddha statue. Later, Sanae decides to become Squid Girl's personal bodyguard so she can be around her all the time. However, her 'SP' self soon comes into conflict with her old perverted self. In another dream, Mini Squid Girl finds herself blown into the wilderness and goes on an adventure to find her way back home.
Ayumi's father invites the Aizawas to have dinner at his house, where Squid Girl and Eiko find his unique hospitality to be quite awkward. Later, Squid Girl falls down the stairs and loses her memory. As the others try to make up memories for her, she regains them after she tries to force her hat off and sees her life flash before her eyes. Later, Squid Girl decides to set up an 'Invasion Club' with Kiyomi and her friends, where they go out to various places to 'invade'. Squid Girl becomes worried about the club when Kiyomi becomes absent with a cold, but they all decide to visit her and invade her house too.
As Squid Girl is put in charge of the house whilst everyone is away, she mistakes a burglar for Chizuru's father. After falling into another trap, Squid Girl tries to give up her craving for shrimp, but finds it hard to resist temptation. Later, both Squid Girl and Sanae collapse with heat stroke, with Squid Girl becoming paranoid over what'll happen should Sanae recover first.
A girl named Risa asks Squid Girl and Eiko to play House with her, which becomes more complicated when Sanae and Kiyomi get cast as Squid Girl's lovers. Later, Eiko and Chizuru give Squid Girl a bag and schedule planner for her to make use out of, though she finds things don't always go to her scheduled plans. On the weekend, the Aizawas take Squid Girl to an amusement park they went to as kids, only to find it is closing down and the only ride left are the teacups. Despite the limited rides, the gang decides to stay with the park until the end, giving Eiko memories of being with her parents.
As the Aizawas get together to have yakiniku, between Squid Girl and Chizuru, Eiko can't get any beef for herself. Wanting to better handle herself around flirtatious boys, Ayumi takes some self-defense lessons from Chizuru, who demonstrates her techniques on Goro. On an extremely hot day, the Three Stooges equip the Lemon with a super powered air conditioner to attract customers, which soon turns the beach into a Winter wonderland, which quickly turns into a blizzard.
As Sanae practises hypnotism in the hopes of hypnotising Squid Girl, the others play along with her. Although Sanae fails to make it work, Squid Girl is actually able to make it work, only to discover the coin she had been using was actually a device made by the Three Stooges. Later, the Southern Winds owner joins forces with the Three Stooges to make a robotic Squid Girl to once again challenge the real deal. Although it proves to be a match for Squid Girl, its technical shortcomings lead to its loss. Later, Squid Girl tries to make an effort to become more evil, but becomes concerned when Chizuru doesn't react to her misbehavings. The two end up going shopping and going to a restaurant together, where Chizuru expresses her wishes to be good friends with Squid Girl.
Squid Girl asks the Lemon to help her invasion club practise for proper invasions, though really she wants to test her ability to invade without Chizuru around. After Squid Girl gets into a fight with Eiko, they decide to stop talking to each other. As everyone attends a summer festival, Squid Girl ends up getting separated from her friends. As a shower hits, Eiko decides to search for her and meets Kozue, who helps her find and make up with Squid Girl.