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.