Texhnolyze takes place in the city of Lux, a man-made underground city that has crumbled after years of neglect and lack of repairs. Citizens of Lux have come to refer to their home as simply "The City" and treat it as though it has a mind and will of its own. Three major factions battle to control Lux: Organo, a group of "professionals" who collaborate with the criminal underworld that controls Texhnolyze (prosthetics), the Salvation Union, a populist group that seeks to disrupt Organo's business, and Racan, a collection of young individuals with Texhnolyzes that use their abilities for personal gain. Ichise was once an orphan who has made a place for himself in Lux as a prize fighter. One day, a fight promoter grows angry with him and the altercation that follows results in Ichise losing an arm and a leg. Before death can take him, Ichise is found by the scientist Eriko Kamata, who uses him as a test subject for her newly designed Texhnolyze. With these powerful new limbs at his disposal, Ichise begins to work for Oonishi, the leader of Organo. He soon meets a mysterious young girl, Ran, who has the power to see possible futures. Together, they soon realize that Lux is on the brink of war and collapse, and that they may be the only ones who can save The City.

Ikta Solork is a carefree young man who only wants two things in life: a woman on his arm and a place to nap. Unfortunately, his peaceful life is destroyed when war breaks out between the Katjvarna Empire and the neighboring Republic of Kioka. Ikta and his childhood friend, Yatorishino Igsem, join the army as military officers, where they meet the infantryman Matthew Tetojirichi, the sniper Torway Remion, and the medic Haroma Becker on a boat heading for the military exam site. However, after a rogue storm sinks their vessel, the five of them end up in enemy territory near a military outpost. There, they discover that the heir to the Katjvarnan throne, Princess Chamille Kitora Katjvanmaninik, has been taken hostage. The five are able to rescue her, and as a reward, each one of them is granted the title of Imperial Knight—one of the highest honors a soldier can receive. It seems that Ikta will have to put his dream of tranquility on hold, as he must now become the hero he never wanted to be.

Keima Katsuragi, known online as the legendary "God of Conquest," can conquer any girl's heart—in dating sim games, at least. In reality, he opts for the two-dimensional world of gaming over real life because he is an unhealthily obsessed otaku of galge games (a type of Japanese video game centered on interactions with attractive girls). When he arrogantly accepts an anonymous offer to prove his supremacy at dating sim games, Keima is misled into aiding a naïve and impish demon from hell named Elucia "Elsie" de Lute Ima with her mission: retrieving runaway evil spirits who have escaped from hell and scattered themselves throughout the human world. Keima discovers that the only way to capture these spirits is to conquer what he hates the most: the unpredictable hearts of three-dimensional girls! Shackled to Elsie via a deadly collar, Keima now has his title of "God of Conquest" put to the ultimate test as he is forced to navigate through the hearts of a multitude of real-life girls. [Written by MAL Rewrite]

The famous "Seven Wonders" that every school seems to have are a staple of Japanese urban legends. One of the most well-known of these tales is that of Hanako-san: the ghost of a young girl who haunts the school's bathrooms. Kamome Academy has its own version of Hanako-san's legend. Rumors claim that if one successfully manages to summon Hanako-san, she will grant her summoner any wish. Lured by the gossip, many people have tried to call upon her, yet every attempt has failed. However, when Nene Yashiro, a girl hoping for romantic fortune, dares to summon Hanako-san, she discovers that the rumored "girl" is actually a boy! After a series of unfortunate events involving Nene's romantic desires, she is unwillingly entangled in the world of the supernatural, becoming Hanako-kun's assistant. Soon, she finds out about Hanako-kun's lesser-known duty: maintaining the fragile balance between mortals and apparitions. [Written by MAL Rewrite]