Aoyama's classmates often mock him for possessing a knowledge beyond his years. Recently, he has taken a liking to a kind woman he met at the dentist's office. Suddenly, penguins start showing up in his neighborhood without any explanation. Aoyama decides to investigate this bizarre happening with the help of his crush. During their search, they come across a floating sphere dubbed "The Sea" which engulfs anything that enters it. The only way to destroy it is by using the creatures that caused chaos in the first place. Unfortunately, the destruction comes at a terrible price. Penguin Highway follows Aoyama's journey to unravel the mystery of the penguins while overcoming various obstacles.