After regaining her squid-like abilities, Ika Musume plans to resume her self-appointed mission to destroy all of humanity. However, her carefree job as a waitress in the Lemon beach house meant she cannot help but laze around during her spare time! On top of that, she is saddled with many problems, such as being pursued by a group of alien-obsessed individuals and catching the interest of a crazy girl. Picking up after the conclusion of the first season, Shinryaku!? Ika Musume follows the hilarious life of Ika Musume as she plots her next invasion of the surface world.

After the noble Kappa Kingdom falls to the Otter Empire, the Kappa prince Keppi loses much of his power and becomes helpless against the unseen Kapa-zombies. These zombies plague the world, and are the creations of the Otters and manifestations of people's deepest desires. With no other choice, Keppi must rely on three young boys: Kazuki Yasaka, who must carry a box with him wherever he goes; Enta Jinnai, Kazuki's childhood friend; and Tooi Kuji, a delinquent and a school truant. By having the mythical organ called a shirikodama removed from them, the boys are able to become Kappa themselves and fight the Kapa-zombies. However, to defeat them, the boys must connect with each other via their minds, bodies, and—most importantly—secrets. As the Kappa Kingdom relies on these boys, they must reveal themselves as they have never done before, all the while learning that connections are fragile and truly precious things.

When aliens known as the Oni threaten to invade the Earth, they promise to leave under one condition—a randomly-chosen human must win a one-on-one game of tag against Lum, the beautiful daughter of the Oni leader. The lucky person selected happens to be the lustful and unlucky high schooler Ataru Moroboshi. Given 10 days to attempt to grab Lum's horns, Ataru realizes how impossible the challenge is as he is faced with Lum's extraterrestrial powers. Motivated by a promise of marriage from his childhood friend Shinobu Miyake, Ataru manages to catch Lum off guard. He mistakenly grabs hold of her bikini top first, but he eventually achieves his true goal. Although the game is over, Lum misunderstands that she is the one whom Ataru wants to marry, and she decides to move in with him. The poor student constantly tries to shake off the clingy Lum while doing his best to reconcile with his desired fiancée. After Ataru's heroic feat results in such a disastrous outcome, it is questionable whether luck will ever be on his side.

The mysterious, yellow-masked Storyteller is a man whose true name and origin are both unknown. He appears at dusk where children gather and recites sinister tales based on Japanese urban legends, to which his young audience eerily intakes. However, the Storyteller is no ordinary teller of tales. He incorporates a kamishibai, a traditional paper-scrolling device, to add visuals to his already demented narration. A series of short horror stories, Yami Shibai begins with a bachelor who, after moving into a new apartment, immediately starts sensing a malevolent glare being pressed into him. A single talisman rests on his ceiling, but he has no way of knowing it is one of the few safeguards that separate him from a bottomless pit of suffering. Each story is more terrifying, more appalling, and more sickening than the last as the Storyteller's audience find themselves being sucked into the vicious world of his words.