The story begins with the TLT assualt team, Night Raiders, investigating a tunnel somewhere in the suburbs of Japan. Headed by Captain Eisuke Wakura and Vice Captain Saijyo Nagi, Night Raiders was en elite team that fights Space Beasts without the knowledge of the Japanese citizens. The recent appearance of the Space Beasts led to the creation of the secret organization, TLT. TLT Director Matsunaga one day hired a civilian volunteer rescuer name Komon Kazuki to become a member of Night Raiders. Leaving Komon's girlfriend, Riko and his family, Komon trained in the secret TLT base located in a dam for two months. When Komon is ready to work, Night Raiders Vice Captain Saijyo Nagi became his superior and his partner. Together they witnessed and came to know Ultraman Nexus' deunamist or human host, a photographer, Jun Himeya, the appearance of the Dark Ultraman Faust and his human host, Night Raiders' former member and Nagi's boyfriend, Mizorogi Shinya. The battle between Nexus and Faust led to the death of the latter and Jun Himeya passing the spark to another deunamist, a teenager named Ren Senjyu. Ren is not an ordinary teenager. He is a product of human cloning of a secret organization, Project Prometheus.But his physical ability is deteriorating due to DNA lapses so in the end, Ren passes on the spark to the third deunamist- Saijyo Nagi.
As the story goes, it is revealed that the real enemy is within the TLT base waiting for the right time to emerge. In the end Komon recieved the spark from Nagi and became the deunamist for Nexus and saved the World from destruction.
Unlike the older Ultraman versions made by Tsuburaya Productions, Ultraman Nexus mainly caters more to adult audience. Indeed this Series is a must-see one.