A large-scale catastrophe predicted to follow (Giant) First Impact and Second Impact. It was officially explained that Third Impact would be caused by contact between an Angel and Adam kept underground below Tokyo-3, and that the Evangelions and NERV existed to prevent this from happening. However, the objective of the Instrumentality Project was actually to initiate Third Impact.

Source: The End of Evangelion : Glossary contained within The End of Evangelion - Theatrical Program.

When humanity discovered the angel Adam in the Antarctic, the attempt to shrink him down to embryo form caused a devastating release of energy, the cover-up was that it was a large meteor impact, it was the second most destructive since an asteroid collided with Earth 4 billion years ago (which resulted in a large chunk of the Earth to fly into space, where it became the Moon), thus was dubbed Second Impact.

Few people in the world knew the true cause of Second Impact, it is even possible that the angels were in some way the cause of First Impact too (the large cavern Adam was discovered in was code named "white moon", it is possible that the moon is this white moon and linked to Adam like how the black moon is linked to Lilith). What was also known by these people was yet another catastrophic event, which they referred to as Third Impact.

Third Impact would be caused when Adam, the source of life, comes into contact with an angel. Kaworu said that only one life form can inherit the Earth, Third Impact would mean salvation for the life form that merged, and the end for all other life.

The Evangelions were created with the story of protecting Earth against the angels, beyond SEELE few knew about what the angels really were, not even governments, so they provided the funding. The people working for NERV, who knew about Second Impact believed that they were working to stop Third Impact. It was, however, SEELE's plan that the Evangelions instigate Third Impact, only with their own scenario.

The Human Complementation Project would evolve humanity far beyond what they are, to remove the AT field between people so that all could become one, not only that but would elevate themselves to the level of God.

Gendou Ikari had different plans for Third Impact, intending to use it in order to be reunited with his wife Yui Ikari.

However the two plans conflicted and the result was that the direction of Third Impact was led by Shinji Ikari. SEELE had begun their plan, launching the Mass Produced Evangelions to destroy the remaining NERV units, killing Asuka Langley Sohryu. Shinji intended to destroy EVA-01 to stop Third Impact (it was an integral part of both plans), he tried to summon the Lance of Longinus to destroy the Eva, but it stopped next to him, the mass produced Evas formed an image of the Tree of Life focussing on Eva-01 and the lance. SEELE started the ritual.

Rei ultimately rejected Gendou, she took Adam and merged with Lilith, thus Third Impact began, using the forbidden combination of Adam and Lilith. Rei/Lilith grew towards the Evas, and Shinji Ikari. The Lance of Longinus envelops EVA-01's core and turns into the Tree of Life. A large explosion extending from Japan released the Geofront which in reality was the egg of Lilith, the black moon. Shinji is frightened and screams, when Rei/Lilith changes her face to show that of Kaworu, this calms Shinji and he starts being asked questions about what he wants. Shinji has been chosen to decide the fate of humanity (it is unknown if it is Rei, Lilith, Yui or Kaworu asking these questions, if it is a mix of them, or if it is something else but the point of the questions is to determine what Shinji wants, what he thinks is best for himself will decide the fate of humanity).

Shinji has a lot of things going on in his head, trying to judge what he thinks of others, himself, what he wants. In the end when he realises the pain of the real world he decides that everyone should die. At this point the anti-AT field emitted by Rei/Lilith and the EVAs expands, covering the world. Everyone's AT field is destroyed, their bodies turn into LCL and their souls float up to the black moon and into Lilith/Rei.

Shinji goes through a lot of philosophical questions, he sees different possibilities for worlds, then he is in the sea of LCL, where the AT field doesn't exist, where you can't tell one person from another, the world without the thing that caused him pain, brings him true loneliness, it is a dead world. It isn't what he thought it would be, but for people to be separate again means restoring the AT field, returning the fear of other people, of not knowing them. He understands that even after running away, from his father, from NERV, from people themselves, things don't get better. He understands that though the AT field can bring hate, fear and loneliness, it can also bring love, without it, there is nothing.

With his decision to restore the AT field the giant Rei/Lilith falls apart, the souls of humanity spill out orbiting the Earth, the LCL floods into the seas, the EVA series die and fall to Earth.

People can return if they have the will to return.

Third Impact occurred and failed to produce the plans envisioned by Gendou or SEELE, leaving humanity left with a post apocalyptic world. However, it did provide humanity with an Ark to survive the catastrophe that would otherwise have destroyed them all.

Note: While there is a lot of what happened in End of Eva, it is not supposed to explain a lot of the other events and things that happen, it is just a description about Third Impact itself, The End of Evangelion is the place for a full write up about the movie.

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