The story is set in a village in the southern Japanese prefecture of Kōchi during World War II. Even in this remote mountainous area, the perception of American and British people as "brutes" has taken root, due to the deaths and injuries among the villagers' relatives. A elementary schoolgirl named Eiko transfers from the city of Yokohama to this village. Eiko happens to have blue eyes from her American father, and her classmates make no attempt to rein in their bullying. Other than Eiko's homeroom teacher Akiko, even the teachers view Eiko the same way that the children do. However, a boy named Kenta views Eiko more with curiosity than with hostility. The children's lives change as the injured father of one of Kenta's classmates returns from the battlefield and news of more casualties arrives in the village.

The bustling metropolis of Kansai, where cybernetic screens litter the neon landscape, may seem like a technological utopia at first glance. But in the dark alleys around the brightly-lit buildings, an unforgiving criminal underbelly still exists in the form of fugitives known as "Akudama." No stranger to these individuals, Kansai police begin the countdown to the public execution of an infamous Akudama "Cutthroat," guilty of killing 999 people. However, a mysterious message is sent to several elite Akudama, enlisting them to free Cutthroat for a substantial amount of money. An invisible hand seeks to gather these dangerous personas in one place, ensuring that the execution is well underway to becoming a full-blown bloodbath. [Written by MAL Rewrite]

The series features colorful stop-motion mascot characters made out of pipe cleaners. In Japanese, "aiseki" refers to the situation of sharing a table at a restaurant with a person you don't know. The show is surreal datsuryoku-kei comedy with a variety of male guest voice actors who banter with Fuyumi and Haruko at a table in the Mongol Cafe.

A summary of Ai Shoujo Pollyanna Monogatari full series aired as TV Specials in 2001.