The story of Evangelion primarily begins in 2000 with the "Second Impact", a global cataclysm which almost completely destroyed Antarctica and led to the deaths of half the human population of Earth. The Impact is believed by the public at large and even most of Nerv to have been the impact of a meteorite landing in Antarctica, causing devastating tsunamis and a change in the Earth's axial tilt (leading to global climate change) and subsequent geopolitical unrest, nuclear war (such as the nuking of Tokyo), and general economic distress. Later, Second Impact is revealed to be the result of contact with and experimentation on the first of what are collectively dubbed the Angels: Adam. The experiments were sponsored by the mysterious organization Seele, and carried out by the research organization Gehirn.

In the year 2010, Gehirn had accomplished a number of its scientific and engineering goals and corporately changed into the paramilitary organization Nerv which is headquartered in Tokyo-3, a militarized civilian city located on one of the last dry sections of Japan; Nerv's central mission is to locate the remaining Angels predicted by Seele, and to destroy them. However, Nerv has its own secret agenda, as directed by its Machiavellian commander Gendo Ikari: the Human Instrumentality Project, which, according to Gendo in episode 25, is the task of uniting all human minds into one global spiritual entity. Associated with Nerv is the Marduk Institute, which has the task of selecting the pilots for the Evas, the most capable being children conceived after the Second Impact (14 year olds). The institute consists of Commander Ikari, and Nerv's chief scientist Ritsuko Akagi; supporting the two are 108 companies which are all revealed to be ghost companies.