The Second Impact is a cataclysmic event which occurred in Antarctica on September 13, 2000. It was caused by an experiment conducted on Adam by a group of scientists led by Dr. Katsuragi. The experiment reawakened Adam, generating an explosion that melted the Antarctic ice caps and shifted the Earth's axis. The scientists subdued Adam, but they were only successful in limiting the damage and averting humanity's complete extinction. The resulting sea level rise, tsunamis, and armed conflicts eventually wiped out half of the human population, and had massive geopolitical implications for the nations of the 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 is 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 in Antarctica, a group of human scientists led by Dr. Katsuragi discovered the White Moon, Adam, and its Lance of Longinus. Dr. Katsuragi had theories about Super Solenoid engines that were, at the time, considered unserious and outlandish. Also part of the expedition was Gendo Ikari, and Dr. Katsuragi's teenaged daughter Misato.
The Katsuragi expedition was actually backed by a shadow organization known as SEELE, which had secretly dominated the governments of Earth for a millennium.
Second Impact and its Aftermath
After excavating Adam, the Katsuragi Expedition planned a contact experiment that would merge human DNA with Adam. Gendo departed from Antarctica just before the experiment began.
The attempted merger reawakened Adam with cataclysmic results. The Anti-A.T. Field generated by the reanimated Seed of Life caused a massive explosion that eradicated all life in Antarctica. 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 explosion shifted the axis of the Earth's rotation and melted the Antarctic ice caps. Before his death, Dr. Katsuragi placed his daughter Misato in an escape capsule. She was the sole survivor of the Katsuragi expedition.
The melting of the Antarctic ice caps caused tsunamis and a rise in sea levels, immediately killing more than two billion people in the Southern Hemisphere. The disaster also had massive environmental and geopolitical effects. After decades of prosperity, the nations of Earth suddenly faced intense resource scarcity and massive refugee migrations.
Upheaval Across the Globe
While spared the immediate destruction experienced in the Southern Hemisphere, the nations of the Northern Hemisphere also suffered severe damage. Two days after Second Impact, on September 15, skirmishes between refugees led to a conflict between India and Pakistan that included a nuclear exchange between the two nations. On September 20, an N-bomb was dropped on Tokyo, killing 500,000 people. Fighting raged across the planet until the Valentine Cease-Fire treaty was signed on February 14, 2001.
By the time the peace treaty was signed, half of the Earth's human population had been wiped out. Many coastal regions and islands were completely submerged by the rising oceans.
The immense political 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 U.N. Unbeknownst to most of humanity, the United Nations was also firmly under the control of SEELE.
In the aftermath of Second Impact and the resulting wars, the Japanese government abandoned any hope of restoring old Tokyo. Instead, the Japanese capital was moved to Matsumoto City in Nagano Prefecture, which was renamed "Tokyo-2." Construction of the new capital began in 2001 and by 2003, Tokyo-2 was functioning as the center of Japanese governance.
Even after the wars, the environmental effects of Second Impact remained. The shift in the Earth's rotational axis changed the way seasons experienced across the globe. In Japan, fall and winter disappeared, as the country was fixed in a perpetual state of summer. The singing of cicadas, long a hallmark of Japanese summers, became a year-long fixture.
Most of what was left of humanity was never told about White Moon, Adam, or the Lance of Longinus.
Instead, the survivors were told that the Second Impact was caused by a meteorite impact in Antarctica. The meteorite was supposedly too small (about 10 centimeters or 4 inches wide) and too fast (95% of the speed of light) to be detected. Fifteen minutes before the impact, it was supposedly sighted by the Mexican astronomer Ceimoa Nan.
Some individuals unassociated with SEELE or its affiliates became suspicious of the cover-up, including Professor Kozo Fuyutsuki.
Their suspicion was more than warranted. In truth, the Second Impact was not an accident, but an intentional act by SEELE. Adhering to 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 contact experiment began, knowing full well what its destructive results would be.
How the Second Impact occurred in the Rebuild series is unknown, but there appeared to be four "Adams" during the event. During the start of the Third Impact in Evangelion 2.0: You Can (Not) Advance the event is described as a "continuation of the Second Impact." The implications are unknown, as there was an explosion during the Second Impact, but no explosion during the Near Third Impact.
Notes and references
- Also, in this episode, Ritsuko’s dialogue reveals that the Second Impact occurred when the First Angel exploded 15 years ago. Make note of the fact that Misato turns away while Ritsuko explains this. The notes in the textbook in this scene also explain that the First Impact is what is also called the Giant Impact, which happened 4 billion years ago when an asteroid struck Earth. In other words, it is called the Second Impact because it is the first enormous impact since the Giant Impact. - Platinum Episode Commentaries