The third impact lore

First Impact occurred in prehistoric times when the Black Moon, a giant spherical object, collided with the Earth in what is now the Hakone region of Japan. The collision caused an explosion that launched a massive amount of material from Earth into orbit. This orbiting debris eventually coalesced into Earth's only moon. The Black Moon was the vessel that carried Lilith, one of the Seeds of Life sent out into the universe by the First Ancestral Race. However, Lilith's arrival on Earth was an accident. When Lilith landed on Earth, the Seed of Life intended for Earth, Adam, was already on the planet. Adam had landed in the White Moon in what is now Antarctica. Having two Seeds of Life on the same planet violated an ancient rule of the First Ancestral Race. Under that rule, only one Seed of Life was allowed to populate any one planet at a time. Lances of Longinus, which can disable a Seed of Life, were sent to accompany each seed in order to enforce this rule. However, Lilith's lance was seemingly lost during First Impact. This meant that Adam had to be placed into suspended animation by its Lance of Longinus in order to comply with the rule. With Adam incapacitated, the progeny of Lilith, including humans, flourished. This denied the children of Adam, the Angels, their rightful inheritance: the chance to populate the Earth. Billions of years later, a group of human scientists led by Dr. Katsuragi discovered the White Moon, Adam, and its Lance of Longinus in Antarctica. The so-called "Katsuragi Expedition" then attempted an experiment to merge human DNA with Adam. This merger reawakened Adam, who generated a powerful Anti-A.T. Field. This caused a massive explosion, which eradicated all life in Antarctica and melted the polar ice caps. The scientists used the Lance of Longinus to subdue Adam and revert it to an embryonic state, but it was too late. The damage was done. The melting of the Antarctic ice caps caused sea levels to rise around the globe, immediately killing more than two billion people in the Southern Hemisphere. The worldwide rise in sea levels had massive environmental and geopolitical effects. War and ethnic conflicts broke out across the planet, as the nations of Earth dealt faced intense resource scarcity and massive refugee migrations. When all was said and done, Second Impact killed half of the human population on the planet. Using the Magi computer systems at five other NERV bases, SEELE attempts to hack into the Magi system in Tokyo-3. If they could control the computer system for NERV headquarters, they could capture Unit-01 remotely. However, Dr. Ritsuko Akagi erects a firewall to defeat the SEELE hacking attempt. Resorting to the use of force, SEELE informs the Japanese government that NERV intends to render humanity extinct by beginning Third Impact. In response, the Japanese prime minister orders the Japanese Strategic Self Defense Force to attack and occupy NERV Headquarters. The priority for the JSSDF mission is to kill the three remaining Evangelion pilots and take possession of Unit-01. JSSDF forces ruthlessly kill many members of NERV, even executing non-combatants and individuals attempting to surrender. However, a reawakened Asuka, piloting Unit-02, is able to destroy most of the JSSDF attack force. Abandoning the JSSDF, SEELE deploys nine Mass Production Evangelions to eliminate Unit-02. After a protracted battle, the automated Evangelions use replicas of the Lance of Longinus to brutally kill Asuka and render Unit-02 useless. Major Misato Katsuragi is killed delivering Shinji safely to Unit-01. When activated, the purple Evangelion generates an A.T. field so powerful that it manifests into wings of light. Shinji screams in agony seeing the brutalized corpse of Unit-02 below. This spurs the Lance of Longinus, on the surface of the moon, to rapidly return to Earth. It stops just short of penetrating Unit-01's throat. The Mass Production Evangelions take custody of Unit-01. The automated Evangelions use replica Lances of Longinus crucify the purple Evangelion and impose the stigmata of Christ on its hands. The Mass Production Evangelions then assume a formation around Unit-01, and begin to overload their S² engines to create an Anti-A.T. Field. This conjures an image of the Sephirotic Tree of Life, which symbolizes the ten aspects of creation in the Kabbalah tradition. Finally, the S² engines of the Mass Production Evangelions overload, causing an eye-shaped explosion that engulfs much of Japan. The explosion also exposes the Black Moon for the first time in billions of years. Knowing that his time to begin Third Impact on his own terms is limited, Gendo takes Rei to Terminal Dogma. He plans to merge the embryonic Adam, which he embedded in his own hand, with Rei, the vessel for Lilith's soul. Rei absorbs Adam into her body. However, Rei rejects Gendo's bid to dictate the terms of Instrumentality, and instead chooses Shinji to do so. After absorbing Rei, Lilith transforms into a gigantic white being bearing Rei's visage. The giant Lilith/Rei ascends into the sky. The nine Mass Production Evangelions assume a new formation centered around Lilith/Rei. The automated Evangelions merge with her, each of them mutating to possess Rei's face. This drives Shinji to lose his already weak grasp on sanity. Lilith/Rei mutates into Kaworu, which calms Shinji. The Lance of Longinus penetrates Unit-01's core, transforming the purple Evangelion into a physical manifestation of the Tree of Life. Fuyutsuki observes that because the newly formed Unit-01/Tree of Life possesses both the Fruit of Life from the Angels and the Fruit of Knowledge from humanity, it has become an equivalent to God. He declares the future of mankind now rests in Shinji's hands. Lilith takes the form of Rei again, and she asks Shinji what he wishes for as he enters Instrumentality. After facing Asuka, Misato and Rei, and Asuka's refusal to serve as his escape, Shinji decides that both he and humanity should perish. Responding to Shinji's wish, Lilith/Rei absorbs Unit-01/The Tree of Life through a third eye that emerges on her forehead. This allows her to create an Anti-A.T. Field so powerful that humans are unable to maintain their physical form. People all over the planet dissolve into LCL, the primordial soup from which all Lilith-based life originated. Every human soul is collected within the Black Moon and returns to the Chamber of Guf. There, the collected souls merge into a single life form, which completes Human Instrumentality. Each soul leaves behind a green cross of light, billions of which cover the face of the Earth. It is unclear whether Gendo was denied the opportunity to join in Instrumentality by Lilith/Rei as punishment for his deeds. Though theoretically one with all of humanity, Shinji finds that Instrumentality is a lonely form of existence. He realizes that the connections he made with people in the pre-Instrumentality world brought him real joy. Even at the risk of getting hurt again, Shinji wishes for another chance to find that joy by being with people. He decides to reject Instrumentality in order to give himself that chance. Shinji's decision causes Lilith/Rei's Anti-A.T. Field to disappear and be replaced by an A.T. Field. Lilith/Rei's body begins to decay. Her arms and head fall off her body as she falls to the planet's surface. A laceration appears on her neck, generating an enormous fountain of LCL that reaches the moon. Unit-01, no longer the Tree of Life, bursts out of one of Lilith/Rei's eyes and removes the Lance of Longinus from its core. Unit-01 becomes petrified, and floats into deep space along with the Lance of Longinus. The Black Moon deteriorates, eventually exploding. All of the souls contained within the Chamber of Guf are released and return to the planet's surface. The Mass Production Evangelions whither away and fall to the Earth. Pieces of Lilith/Rei's body, including her head and hands, crash upon the surface. The return of A.T. Fields allows Shinji to regain his physical form. He finds himself wading in a sea of LCL. Third Impact ends.