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.

Souta runs into his old childhood friend, Shoukanji Kikuno, who loves to spoil him. Quest Dorm is in shatters, and Kikuno asks the school elder, Ryuukishibara Tsumugi, and the student council president, Seiteikouji Mimori for help. They ask for the dorm to be rebuilt, but...

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...

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...

Souta promises to go on a date with Akane, and the rest of Quest Dorm finds out about it, and wants to go as well. Nanami stays back at home, but Souta has to go on a date with Megumu, Akane, Rin, and Kikuno.

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...

Hatagaya Academy goes on a trip near the ocean, and Souta meets Daishikyougawa Kurumiko there. Souta enlists the help Mimori Seiteikouji, the granddaughter of the chair. Souta and Mimori go on a date as compensation.

Souta returns home with Kikuno during summer break, and is spoiled by her. Ruri shows up all of a sudden and takes him away. He ends up at Akane's house. Everyone from Quest Dorm is worried about him and shows up too, except Nanami...

Everyone from Quest Dorm goes to Nanami's home country, the Principality of Bladefield, and runs into Nanami's little sister Hakua, and the crown prince. Then there's big news about Hakua and Nanami. Then No. 0 talks to Hatate about the founding fairy tail of the country.

Souta recommends the Quest Dorm enters the Miss Hatagaya Academy Beauty Contest. Nanami gives a speech to cheer up Souta, and wins a festival pass which makes everything free as long as she is with Souta. They meet a girl who is running from something.

The mysterious girl is idol Serika Ginyuuin. During her concert Souta's powers increase and time freezes. No. 0 tells Souta he must leave or the world will be destroyed. Souta erases Quest Dorm's memories of him, but Nanami is unaffected and remembers.

Souta fights the Angelus Gemini to protect his world by placing 'Death Flag' on his enemies. Nanami learns from Riru how she is linked to Souta, and takes the Quest Dorm members to help Souta fight.

Souta regains his memory and learns he knew the girls once before, but had Laplace's Demon save them. Souta and the girls fight the Premium Ambriel, but his death flag breaks and he awakes in the real world where he learns more about his past.