Kanata no Astra follows a group of teenagers whose planned camp on the distant planet McPa turns into a desperate survival mission. In the year 2063, when space travel is feasible and commercially available, the cheerful Aries Spring arrives at the spaceport only to have her purse suddenly snatched by a reckless thief. Luckily, the athletic Kanata Hoshijima retrieves it for her, and Aries soon discovers that he is among the students traveling with her on the excursion as team B-5.
When the group reaches their campsite, a strange sphere of black light hurls them into the vast reaches of outer space. Stranded with seemingly no hope, they find an abandoned ship nearby that offers a way back home, but the situation grows far worse when they realize they are not close to the campsite at all and are in fact thousands of light-years away from Earth.
With limited supplies and no clear explanation for the disaster, the nine members must cautiously manage their resources, protect one another, and maintain their strength as they set out on a dangerous voyage aboard their new ship, the Astra. As they cross the darkness of space together, the mystery behind their sudden displacement slowly begins to come into focus.