The Second Impact is a cataclysmic event which occurred in Antarctica on September 13, 2000. It was caused by the Contact Experiment conducted on Adam by a group of scientists led by Dr. Katsuragi. The experiment reawakened Adam, who generated a massive Anti-A.T. Field. The Anti-A.T. Field caused an explosion that melted the Antarctic ice caps and shifted the Earth's axis. The resulting sea level rise, tsunamis, and climate change eventually wiped out half of the human population and had massive geopolitical implications on the nations of Earth.
As the term implies, Second Impact is the second of three major events on Earth involving the intervention of the First Ancestral Race.
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.
The Katsuragi Expedition
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. Dr. Katsuragi possessed theories about Super Solenoid engines that were, at the time, considered outlandish. Also part of the expedition was Gendo Ikari, and Dr. Katsuragi's daughter Misato.
The secret of the Katsuragi expedition is that it was backed by a secret organization known as SEELE. SEELE had dominated the governments of Earth for a millennia.
Second Impact and its Aftermath
After having excavated Adam, the Katsuragi expedition planned an experiment that would merge human DNA with Adam. Gendo departed from Antarctica just before the experiment began.
The experiment reawakened Adam with cataclysmic results. The Anti-A.T. Field generated by the reanimated Adam 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. Before his death, Dr. Katsuragi placed his daughter Misato in an escape capsule. She was the sole survivor of the Katsuragi expedition.
The onset of Second Impact was not an accident, but an intentional act by SEELE. Adhering the prophecies contained in the Dead Sea Scrolls, SEELE sought to reduce Adam to a more manageable embryonic state. This would help prevent contact between Adam and its progeny, the Angels, whose arrival fifteen years later was predicted by the Dead Sea Scrolls. SEELE decided to pursue this plan, despite knowing that its execution would kill billions of people and permanently alter the planet. Gendo had purposefully left Antarctica just before the disaster, knowing what the results of the the contact experiment would be.
Some individuals unassociated with SEELE or its affiliates became suspicious of the cover-up, including Professor Kozo Fuyutsuki.
The cover-up story
What was left of humanity was told that the Second Impact was caused by a massive meteorite impact in Antarctica. Most of the survivors knew nothing of Adam, the Lance of Longinus, or the White Moon.
Officially, there was no Adam and no "contact experiment." According to the cover-up, the Second Impact was caused by the impact of a meteorite that was too small (about 10 centimeters or 4 inches wide) and too fast (95% of the speed of light) to be detected. Fifteen minutes before its impact, it was sighted by the Mexican astronomer Ceimoa Nan.As a result, more than two billion people in the southern hemisphere were immediately killed by the tsunami and rising water level caused by the melted ice. This was the worst disaster mankind had faced in recorded history.Vast environmental damage and global climate changes resulted from Second Impact and the rise in global sea levels. These effects were worldwide, but during the series we are only shown the immediate changes observed in Japan, where the elevated sea levels have caused many old coastal cities to be submerged. Also, Japan has become a country of perpetual summer weather. A subtle hint of this throughout the series is that cicadas are frequently heard in outdoor scenes, even though they would normally only appear in Japan during summer months. Fuyutsuki alludes to this when he mentions first meeting Gendo Ikari when "this country still had seasons" (before Second Impact), and that the loss of the seasons was the worst that Japan had suffered.
Considering the ancient meteorite impact which created Earth's Moon to be the "First" Impact, the public at large officially dubbed this disaster the "Second" Impact in keeping with the cover-up story of a meteorite impact. Several NERV personnel (Ritsuko Akagi, etc.) know the true cause of the explosion but still refer to it as "Second Impact" for the sake of convenience.
Upheaval in the northern hemisphere
The nations of the Northern Hemisphere also suffered severe damage from the flooding and chaos ensued. Two days after the fall of the meteorite, on September 15, 2000, collisions between refugees sparked a war on the India-Pakistan border, and armed conflicts began all over the world. On September 20, an N-bomb was dropped on Tokyo and 500,000 people were killed. Until the Valentine Cease-Fire treaty was signed on February 14, 2001, in order to put a stop to the wars following the Second Impact, hostilities continued all over the world. By the end of these events, the human population of Earth was halved.
The immense changes wrought by the Second Impact led to the expansion of powers held by the United Nations. While many existing nation states—such as the United States, Japan, China, and Germany—continued to exist, the U.N. exercised a much larger role in the daily lives of human beings. The militaries of most of the planet's major nations were brought under the authority of the United Nations. Unbeknownst to most of humanity, the United Nations was now under the control of SEELE.
Transferring to Second Tokyo
The Temporary Government of Japan gave up on restoring the Tokyo that had been destroyed by the N-bomb, and the decision was made to transfer the capital to Matsumoto City in Nagano. Construction of Tokyo 2 began in 2001, and development proceeded rapidly, and by early 2003, Tokyo 2 was fulfilling its function as the capital. In 2005, a second transfer of authority was approved by Congress, and development of Tokyo 3 started.
How the Second Impact occurred in Rebuild is unknown at the time but there were four "Adams" during the event. During the start of the Third Impact in Evangelion 2.0: You Can (Not) Advance the event is called a "continuation of the Second Impact". The implications are sort of unknown as there was an explosion during the Second Impact but no explosion during the Near Third Impact.