Souta Hatate can see 'flags,' the warning signs of choices about to shape someone's future, and that power is what carried the original If Her Flag Breaks. This second part picks up after Souta saves the virtual world of Hatagaya Academy and wakes in the real world, where the real counterparts of the girls he knew are waiting for him along with one he has never met. Souta decides to protect this world too, and the flags start appearing all over again.