Blue Gender takes place in the not too distant future in a world where things have gone terribly wrong for humanity. Humans have been replaced at the top of the food chain by the Blue, a race of bug-like aliens that have colonized Earth and pushed humans aside. A space station, Second Earth, has been constructed as a safe haven for humans, with the hope of one day reclaiming the Earth once more. Yuji Kaido was cryogenically frozen, having been suffering from a disease known as B-Cells. Once awakened, he joins a team of soldiers that have come to Earth to extract him. Unfortunately, nothing goes according to plan as they make their way back to Second Earth. Yuji will have to deal with the horrors of fighting a bloody war as he and the fighters from Second Earth look to survive. Will they be able to win back Earth without losing their humanity?

Yoichi Isagi was mere moments away from scoring a goal that would have sent his high school soccer team to the nationals, but a split-second decision to pass the ball to his teammate cost him that reality. Bitter, confused, and disappointed, Isagi wonders if the outcome would have been different had he not made the pass. When the young striker returns home, an invitation from the Japan Football Union awaits him. Through an arbitrary and biased decision-making process, Isagi is one of three hundred U-18 strikers selected for a controversial project named Blue Lock. The project's ultimate goal is to turn one of the selected players into the star striker for the Japanese national team. To find the best participant, each diamond in the rough must compete against others through a series of solo and team competitions to rise to the top. Putting aside his ethical objections to the project, Isagi feels compelled to fight his way to the top, even if it means ruthlessly crushing the dreams of 299 aspiring young strikers.

Saya Otonashi is a seemingly ordinary girl living a mundane life with her adoptive family in Okinawa City. In fact, her only peculiarities are suffering from anemia and being unable to remember any of her life beyond the previous year. However, Saya's forgotten past quickly comes back to haunt her—one night, she is attacked at school by a creature that feeds on human blood. Just when all hope seems lost, a mysterious man named Haji appears and fends off the creature temporarily. But when her rescuer forces her to drink his blood, Saya suddenly enters a trance and slays the monster with ease, using her own blood as a catalyst. Saya then learns of an organization named Red Shield, founded for the sole purpose of defeating the hellish beasts. Now Saya and Haji must work together with Red Shield to fight these fearsome monsters and unlock the secrets to the girl's past.

60 years ago, a strange case of insomnia struck the population, forcing them to stay awake for more than a full week. The victims, completely sleep deprived, all went mad. To cure this illness, a new medicine was produced, but the side effects turned the patients into vampires. Humanity went to war against this new species and triumphed, but some of the vampires managed to survive. Born from a Human and a Vampire, the main character Mi Liu, The Child of Hope, is to represent the new hope that will connect the two species. Ringleader of a bank robbery, Mi Liu is arrested and transferred to a special prison of the National Defense Agency that monitors Vampires. Trying to break free with Anji, Mi Liu is attacked by strange monsters and he finds out that the prison location corresponds to the birthplace of Vampires, the old capital Blue Town. Why are Vampires trapped in Blue Town? What are those strange monsters attacking them? Our heroes must fight to solve those mysteries. (Source: Emon via ANN)