As we near the end of Evangelion, be prepared for outrageous amounts of action, violence, and sex to end the series...... well, not really. Actually, the series ends with intense psychological introspection and questions the very nature of reality.
Now that the last Angel has been defeated, all that remains is the enigmatic Instrumentality of Man Project which has always been foremost in Gendou's plotting and in the plans of the mysterious Seele. Although seeming to take second stage behind the Evangelion project and the continuous attacks by the Angels, the Project is actually the driving force behind the actions of Gendou and the committee.
In episode 14 ("Seele, Throne of Soul"), it is the "Committee of the Instrumentality of Man Project" that accuses Gendou of covering up the fact that an Angel managed to invade Central Dogma, the Angel which took over Magi like a virus. Does this imply that the committee which controls Nerv and Eva through Gendou is actually primarily related to the Project? Notice also the title of this episode and recall that Eva is referred to as the "throne of the soul" several times throughout the series.
Given that the main purpose of the body which supports Gendou, Nerv, and Eva is the Project, what relation does this have with Eva and the Angels? Perhaps Gendou gives a hint in episode 15:
And what is the relationship between the "children," those capable of piloting Eva who were all born in the year of the Second Impact, and the Project? Again from episode 15 we see:
Does Gendou's late wife, Yui (Shinji's mother), have anything to do with the Project? In episode 21, just one week after her mysterious death:
Somehow, Yui is pivotal in the difference between Gendou's vision and the committee's plans:
And in the following scene, Gendou stands before Unit 1 and speaks as if addressing it:
Recall that Yui disappeared in the "graveyard" of failed Evas and that in episode 16, when Shinji is trapped in Dirac's Sea, he sees his mother and then is saved by Unit 1 under her own power.
Episode 25, which we are seeing today, gives even more insight as to what everything is about.
Something critical, and perhaps UNFATHOMABLE, is happening, something that the past 24 episodes have been building up to.
What is the Instrumentality of Man?
All the minds become one, obtaining peace forever.