I honestly believe that Neon Genesis Evangelion (NGE) TV series (1995-1996), together with The End of Evangelion (EoE) (1997), are ground-breaking anime classics.  The series is notable for an incredible lack of answers, because it is meant for viewers to find their own answers.  Although there is no lack of Evangelion resources on the web, I think it is beneficial for newcomers to get a single and relatively concise explanation of all the major things in NGE and EoE, instead of having to dig through the really resourceful but enormous evageeks.  (The recent Rebuild of Evangelion / New Theatrical Edition (NTE) (2007-2015), although visually far superior, changes the storyline completely by the third movie.  Although this article is not meant for the Rebuild of Evangelion / NTE, parts of it are still relevant.)

Almost everything here originates from evageeks, edited based on my understanding.  The vast information is filtered and organized based on what I consider to be important into this article.

This article is full of SPOILERS, naturally.

First Ancestral Race

Although never mentioned in the series, the role of First Ancestral Race is really important in the world of Evangelion – in simple terms they are the gods.  They send Seeds of Life to different planets in the Milky Way Galaxy.  Each is placed in a carrier vessel known as a Moon along with a Spear of Longinus.  There are two kinds of Seeds of Life: Fruit of Life and Fruit of Knowledge.  Fruit of Life and Fruit of Knowledge are not meant to exist in the same planet – because fusion of these two powers mean attaining god-like powers equivalent to the First Ancestral Race, therefore such a fusion is known as a “forbidden union”.  To prevent this, a Spear of Longinus, a security device, is made to subdue a Seed of Life when needed.

Adam, Lilith and First Impact

A Seed of Life known as Adam, a Fruit of Life, reaches Earth first in a White Moon.  In the First Impact, another Seed of Life known as Lilith, a Fruit of Knowledge, also reaches Earth in a Black Moon by mistake, but loses her Spear of Longinus.  Under the rules set by the First Ancestral Race, the Spear of Longinus that came with Adam subdued him, allowing Lilith to spread life on Earth, creating Lilin, i.e. human.

Dead Sea Scrolls

The Dead Sea Scrolls are a scripture written by the First Ancestral Race, a manual regarding the Seed of Life and the usage of the Spear of Longinus.  They are written prophecy as they remain active even in the current day according to a design of the past.

Second Impact, Adam and Creation of Kaworu

In September 13, 2000, the Seele-funded Katsuragi Expedition discovered Adam, its Spear of Longinus, and the White Moon in Antarctica.  They performed a Contact Experiment to fuse human DNA with Adam, resulting in the creation of Kaworu with the soul of Adam.  They also used the Spear of Longinus to reduce Adam to an embryonic state in order to conceal and protect it from the Adam-born Angels before they awoke.  However, this act caused the Second Impact, which directly and indirectly caused the death of half of the human population.

Angels’ Intentions

Angels (except the 2nd Angel – Lilith) are born from Adam, and carry the Fruit of Life in form of S² Engine.  Some of them are trying to access Lilith and reset all life, and some are trying to recover their progenitor Adam.  Third Impact will occur if an Angel comes in contact with either Lilith (in Terminal Dogma) or Adam.  An Angel-induced Third Impact will wipe out humanity and let the Angels reclaim Earth.

Seele’s Agenda

Seele intends to initiate Third Impact to bring about Human Instrumentality, via the use of Mass Production Evangelions, the Spear of Longinus, Lilith and Evangelion Unit-01.  The actual execution (although eventually aborted by Shinji) is seen in The End of Evangelion.

Human Instrumentality

As a result of human-induced Third Impact, all Lilin (human) souls are united into a single existence within Lilith’s Egg (Black Moon) where no individual existed.  Flaws in every living being would be complemented by the strengths in others, thus filling the gaps and erasing the insecurities in people’s hearts.

Gendo’s Agenda

Gendo wishes to use Instrumentality to reunite with his wife Yui, whose soul is in Evangelion Unit-01, by merging with Rei (with soul of Lilith), Lilith and Adam embryo (fused to his hand).  If Rei III does not reject him, he would have the power to control the instrumentality process.  It is unclear what he plans for the rest of the humanity, but since he says “destruction creates nothing”, probably he may let everyone else emerge from the “ark called EVA” and be free to reembody as individuals, unlike Seele’s intentions.

Gendo tries to get rid of the Spear of Longinus because it is the only thing that would threaten him once he successfully takes control of merged Rei-Adam-Lilith-EVA-01 with god-like powers from both the Fruit of Life and Fruit of Knowledge.

Yui’s Agenda

Yui, as the daughter of a Seele member, knew about Seele’s plans.  In order to preserve human life instead of letting Seele exterminate humanity, she deliberately chose to perform the Contact Experiment on Evangelion Unit-01 and remain inside it for eternity, unbeknownst to Gendo.  She protects Shinji by controlling it, manifesting as berserk incidents, and consuming the S² Engine – Fruit of Life in order to become the eternal proof that humankind existed, even after 5 billion years, when the Earth, the Moon, and even the Sun have disappeared.  As for why it is important for Shinji to witness the Contact Experiment, it is not about seeing her vanish, but to let Shinji eventually realize that she did this for his protection and for humanity, eternally.

Why Seele Sent Kaworu to NERV

Seele sent the final Angel, Kaworu, directly to NERV, hoping that Evangelion Unit-01 will kill it, speeding up Seele’s Agenda.

Why Kaworu Follows Seele’s Instructions

Seele pretended to support the Angels by saying “mankind are the false successors from the Black Moon” and “Angels are the true successors from the lost White Moon”.  They also deceived Kaworu by saying the Angel in Terminal Dogma is Adam, although it is in reality Lilith.

EVA-00’s soul

EVA-00’s soul is Rei I.

Who Killed Kaji

Kaji was not shot by any named character, but by an agent sent by either Seele or Nerv’s intelligence division.

Why mankind is the 18th Angel

It merely means that human is the 18th kind of life form that originated from a Seed of Life on Earth.

Gendo’s Silent Words to Ritsuko

“I needed you”.

What Happened in Third Impact and End of Evangelion

At the beginning of Episode 26′ (i.e. the second half of End of Evangelion), the Mass Produced Evangelions capture Shinji along with Eva-01. With the Spear of Longinus, a ritual is performed that creates an inverted Tree of Life in the sky, and Eva-01 merges with the Tree of Life. The Mass Production Evangelions resonate their A.T. Fields, causing a giant explosion around the GeoFront. In its wake, Lilith’s Black Moon is revealed.  This begins the Third Impact.

Meanwhile, in Terminal Dogma, Gendo attempts to fuse the Adam embryo in his right hand with Rei. Rei rejects Gendo, taking his hand along with Adam’s embryo, and merges with Lilith, thus achieving the “forbidden union of Adam (with Fruit of Life) and Lilith (with Fruit of Knowledge).”  This Rei/Adam/Lilith hybrid being takes the form of a Giant Naked Rei.

Giant Naked Rei begins to merge with EVA-01. During this process, Shinji states: “Nobody cares whether I exist or not… Nothing will change. So, everybody just die.” This wish seems to manifest itself into reality, as Giant Naked Rei proceeds to create an Anti A.T. Field which spreads across the globe, reverting all human into LCL. Ghostly apparitions of Rei appear before everyone.  The liberated souls of humanity are gathered by Giant Naked Rei and funneled into the Black Moon (her “Egg”). When this process is completed, Human Instrumentality begins.

This is clearly not what Gendo had intended, but the Seele council seemed fairly content with the outcome. However, Shinji ultimately rejects Instrumentality, and the Black Moon is destroyed, dissipating the souls back across the Earth and into the oceans. Giant Naked Rei’s body falls apart and descends to Earth.

Yui says people can restore their bodies as long as they imagine themselves within their own heart, so they can return to life in the physical world, regardless of the pain it would inevitably entail. Shinji, and later Asuka, return to the vicinity of Hakone, but the fate of everyone else is left open.

Yui, inside Evangelion Unit-01 and taking the Spear of Longinus, exiled into outer space alone, to be the eternal proof that humankind has existed.  A flashback to her lakeside conversation with Fuyutsuki implies that she planned for this exile all along.

Why Shinji Strangles Asuka

Shinji renounced the world where all hearts had melted into one and accepted each other unconditionally. His desire… to live with ‘others’ — other hearts that would sometimes reject him, even deny him. That is why the first thing he did after coming to his senses was to place his hands around Asuka’s neck. To feel the existence of an ‘other’. To confirm (make sure of) rejection and denial.

End of Evangelion (EoE) vs End of TV (EoTV)

While EoTV takes place in the minds of the characters during Human Instrumentality, EoE is the actual events that show how this happened.  The two are mostly consistent, but at the very end the tone is different – EoTV being positive but EoE being quite negative.  There is also a debate about whether Shinji accepts instrumentality or not in EoTV.  Nevertheless, there is an excellent article that explains the two are actually concurrent – they show the same thing.

Rei’s Ghostly Apparitions

Rei’s ghostly apparitions not only appear when human beings revert back to LCL, but at the end of End of Evangelion after Giant Naked Rei fell apart, and as early as Episode 01 as well.  These can happen because Rei III, after merging Adam and Lilith, is an existence with god-like powers who can transcend time to gaze upon mankind.