The story revolves around Sakis, who is both a descendant and enemy of the gods, becoming involved in an unexpected event that takes place within Lagoonarian airspace. During this occurrence, he discovers not only explosives but also the origins of Abomination. As a result, Sakis embarks on a journey to unravel the secrets surrounding the ancient deities.
Lagoon Engine Einsatz was serialized in the special English edition of the Japanese Newtypes magazine published in the North America, Newtype USA, but it was discontinued after only ten chapters. Serialization in the Japanese magazine started with a two month delay in January 2005 issue.The series was published in English by ADV Manga on December 20, 2005.