Tousuke Rokudou is a first-year attending Aomori High, a school full of delinquents. He is often bullied by his classmates due to his incompatibility with their behavior, the only exceptions being his two good friends who are also social outcasts. Frustrated at the way they are treated, the three wish they could stand up and claim the fun, peaceful school life of their dreams. However, Tousuke's life takes a drastic turn when he receives a package from his late grandfather containing their family heirloom, a scroll said to possess the power to save him from impending danger. Upon holding the scroll, a sudden glow emanates, leaving a strange mark on Tousuke's forehead. Thinking that he's received the means to free himself and his friends from their daily treatment, Tousuke is shocked to find out that its effects are far different than what he had imagined. Although his bullying continues, he realizes that the mark from the scroll acts as a charm, capturing the hearts of delinquent girls—in particular, Ranna Himawari, the strongest of them all.

Arriving in Japan, underground golfer Eve wants nothing more than to play a match against Aoi Amawashi, the "Innocent Tyrant" prodigy that caught her eye. However, the girls, wishing to finally settle the score on who is the better golfer, will have to wait until the conclusion of the All-Japan Girls' High School Gold Doubles Championship. Now competing together for the Raiou Girls' Academy's golf team, Eve and Aoi decide to work together to claim a win for their institution. For a chance at defeating their more challenging opponents, both girls must find a way to further develop their golfing styles. However, dangerous figureheads pull strings in the background, making this high school golf tournament much more serious than it appears. In addition, Eve's illusive past resurfaces, making matters between her and Aoi even more complicated than they already were.

For more than four hundred years, the Takamimi Shrine has stood in Tokyo, enshrining the local goddess: Elda, a magical elf summoned from another world. The immortal elf has been served for 15 generations by the family who summoned her in the Edo period. Now, after Koito Koganei turns 16 years old, this responsibility falls onto her. Serving as Elda's shrine maiden, Koito must balance her responsibilities with her daily school life. This proves to be difficult because Elda is a total social recluse who loves video games, collecting toys, and eating snacks. In an effort to get the lazy shut-in to experience more of the outside world, Koito juggles her time between indulging Elda's various hobbies and getting her to interact with the rest of humanity. Along the way, Koito learns more about the history of the area and what makes the goddess so loved and spoiled by the locals.

In 2008, the Japanese government began hunting people who identify as otaku in an effort to protect the country's culture. In just one week, the enforcement agency known as the SSC captured almost every otaku by force and confiscated their memorabilia. One passionate man calling himself Otaku Hero refuses to allow this agency to do as they please: he raises a resistance army made up of other displaced geeks who band together to help defend their culture. Three years later, the fires of rebellion wane as all hope seems lost for otakus. Spurred on by his ally—the magical girl Anarchy—Otaku Hero commands the resistance in an effort to reunite Anarchy with the other two other magical girls: Blue and Pink. By combining the power of this trio, the resistance may be able to defeat the SSC and save otaku culture for everyone.