Yes this title is indeed referring to the famous piece that is one of Jazz anthems, Take the "A" Train. Continuing "Nemuranai Machi Kara", Sanako and Kawakubo-kun now are no longer enemies (which we can guess from Nemuranai). They've become more or less inseparable now. However currently Kawakubo-kun's life isn't as pleasant as Sana, this boy has really difficult things burdening him...
What can two children do to stay together when adults' problems are standing on their way? Deciding on their own, Sanako and Kawakubo-kun take off into their private adventure.