Top wo Nerae 2! follows the story of Nono, a country girl who dreams of becoming a space pilot (or to be more precise, 'like Nonoriri,' the meaning of which is revealed as the series progresses) who, due to a chance encounter with an actual space pilot finds herself becoming part of the elite Fraternity. Made up of teenage pilots called Topless, and armed with quasi-humanoid weapons called Buster Machines, the Fraternity's mission is to protect the people of the Solar System from attack by swarms of uchuu kaijuu (literally, space monsters).

Chapter 1, the only proper chapter, tells the story of Nono's first meeting with Lal'C - the aforementioned space pilot and a girl that Nono instantly adores, dubbing her oneesama (big sister).