Halo Legends features seven different stories set in the Halo universe, each made by a different studio. The Babysitter follows the Helljumpers, Orbital Drop Shock Troopers who are sent behind enemy lines to perform an assassination. The Duel features the tale of an ancient Arbiter who refused to bow down to the Covenant religion. Branded a heretic, he must now face the consequences of his actions. The Package depicts a group of Spartans, including the Master Chief, who are deployed to infiltrate a Covenant flagship and retrieve a “package” in a secret operation. Origins shows Master Chief and Cortana stranded following the events of Halo 3, with Cortana summarizing the fall of the Forerunners, the defeat of the Flood, and the rise of humanity as well as the events of the Human-Covenant War. Homecoming centers on the Spartan Daisy, who reminisces on her past, and the SPARTAN-II project while evacuating UNSC soldiers pinned down by Covenant forces. Prototype is viewed from the perspective of Marine Sergeant Ghost, who is determined to fight for all he is worth in order to make up for past grievances. Odd One Out is a non-canon parody of Halo featuring Spartan 1337, who suffers from extremely bad luck.

After witnessing his mother's death at a young age, Uryuu Kamihate grew up disillusioned with the gods, dismissing faith in them as utter nonsense. Due to his beliefs, he aims to become a doctor, spending most of his time studying to enter the prestigious Kyoto University. To further his studies, Uryuu searches for a new place to take him in and get away from the noisy environment of the orphanage where he grew up. Chidori Amagami, head priest of the Amagami Shrine, allows him to stay at the Amagami residence. However, Uryuu has to live there with Chidori's three granddaughters—Yae, Yuna, and Asahi—who serve as shrine maidens. Moreover, Chidori has another condition for Uryuu: he has to marry one of the sisters to ensure the shrine's future and one day inherit it. But with Uryuu's goals and outlook naturally clashing against the sisters' beliefs, this already daunting ordeal seems outright impossible.

Demonic activity worldwide has significantly increased due to the involvement and corrupt practices of the Illuminati. To combat the unnatural influx of demons, the Vatican Headquarters decides to hold the annual Exorcist Certification Exam early and allow for as many exorcists as possible to take up the mantle. Straight from the Vatican, one of the most powerful exorcists, Lewin Lightning Light, arrives at True Cross Academy to help prepare the students for the exam. The ease and mastery with which Lewin performs exorcisms quickly impresses Ryuuji Bon Suguro, who has lost his ambition to continue his studies, and Lewin surprisingly accepts him as his apprentice. Amid the worsening situation, twin brothers Rin and Yukio Okumura are sent to locate the recently missing exorcist Shura Kirigakure, who seems to be chained to a decades-long contract with a powerful, immortal demon hiding in Aomori Prefecture's dangerous, snowy mountains.

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.