Boyhood's End is an adventure game following Giovanni, the boy with the lowest human score in the universe, and Campanella, the delinquent genius, and their journey on the galactic railroad regarding the "human" and "inhuman".

The protagonist, Giovanni, has the lowest human score among the entire human race. Every day, he receives "special treatment" for everything including his meals and classes. On top of that, he gets bullied relentlessly by his classmates at the School, both in real life and online.

But one day, everything and everyone in the school starts attacking Giovanni, trying to "remake" him and raise his human score by making him "more human". A senior student, the famously eccentric genius Campanella, reaches out to Giovanni, and they hop onto (and take over) a driverless train on the galactic railroad. And so, Giovanni gets swept up in a journey to find the "Crimson Southern Cross", located at the farthest edge of the universe.

On their journey, the boys will meet great leaders of the past and pull reckless and destructive "pranks" on them all. Through their encounters with the history, twisted mysteries, and various horrors of the world, they will eventually have to confront the end of their own childhood. Oh, did you hear that? The boys are (pointlessly) sounding the train whistle. Looks like it's time for the galactic express to depart.