>>280886107 Now, none of this is ever fully explained in the Anime, movies, or even in the manga. Though the manga has a better view of Gendo getting Adamn into his hand. This is why Evangelion IS a vague anime, because the Worldbuilding is there, but only revealed in extra material and canon games.
The real meat of show is the psychological impact on the protagonists, that have a very limited understating on what's happening and why.
While using Adam and Lilith to create giant clones as weapons capable of battling the Angles (the Evas) Gendo's wife, and Shinji's mother, dies and is consumed by the Lilith clone that would become Eva 01. This makes Shinji a perfect Pilot for the eva, since his mother would accept him fully, giving him better control and more power out of the Clone.
Shinji is despised by his dad, because Gendo, being a misantropic asshole, loved Dr Ikari too much, the only person Gendo accepted into his her, and considered Shinji a competition for her love, but Shinji is too perfect a pilot, due to being young and, again, loved by Doctor Ikari who is now part of the Eva.
All the Angels are actually trying to do is reach Lilith in her ship, which is what Nerv is built above of.
Since, again, nobody that's fighting actually knows anything about this, the story focus more in their minds as they face apocalypsis and the concept of peace as part of instrumentality, peace but at the cost of any will, hopes or desires as a person, vs individualism and development at the cost of challenges.
When the Lilith Clone under Shinji (Eva 01) clashes with Rei fused with Adam at the end, the Impact ocurs and Shinji, in control of the Fake Lilith, gets to decide what happens, since Rei will follow his lead.
The first and second time he just makes the world again, that's the "Rebuild". The world started again with small changes, until finally they move past the the impact and the world of humans continues.
the END.