Daimyouzamurai Mei, a mysterious transfer student, enters Hatagaya Academy class 1-F. It seems she has the same ability to see flags and manipulate them, just like Souta. Meanwhile, class 1-F is split into two groups based on their grades into swimming, and go on a trip to the ocean and the forest. For some reason, Souta's forced to join both trips...
The week long track meet starts. A new member joins them, and everyone works hard to prevent the shut down of Quest Dorm and from Souta to be expelled. Mimori has a large strange list of events, and Souta and the rest work hard to get the MVP position, but something happens that puts them all at risk...
Everyone's about to start their life at Quest Dorm when Akane gets a mysterious android from her family in the shape of a girl named Ninjabayashi Ruri. Meanwhile, Hatagaya Academy's student council president announces the start of a new event, a week long track meet, and then Mimori surprises everyone...
Flag shows the different paths that fate can take. Hatate Souta transfers into Hatagaya Academy, and he can see these flags, and control them. Souta tries to avoid people after what happened in his past, but Nanami notices something was up when Souta stops an accident on his way to school, and then another girl starts to take an interest in him.