It makes sense.
Quick rundown:
SEELE wants to unite all souls to one and make themselves as Gods.
Gendo wants to reunite with his wife, Yui, using Rei's help.
Rei has rejected Gendo because she sees through him, and instead seeks to find herself.
Shinji is borderline suicidal, and doesn't want to do anything.
SEELE and NERV are in open conflict because Gendo won't obey, and SEELE has the upper hand.
These are the major players as it would turn out in the EVA story.
SEELE invades, and seizes the opportunity to start Third Impact right then and there. They plan to use EVA01 (Copy of a God), the MP-Series (also copies of a God), and Shinji, who's suicidal mindset is what they'll use as a catalyst to end all lives on the planet and take their souls.
SEELE commences the ritual, and the end of the world has begun, effectively.
Gendo is looking to hitch a ride on this to get to Yui using Rei's help. Rei however, senses Shinji's pain, and only takes Adam into herself, and leaves Gendo for dead.
Rei enters her original body, Lilith, and seeks to help Shinji. Rei does this by assimilating the MP-series, so that Rei effectively becomes one half of the Third Impact engine, while Shinji is the other.
Too little too late, and the entirety of mankind is reduced to nothing but their souls, and are absorbed into the third impact medium, which has become Rei.
From hereon out, Rei and Shinji talk, and Rei is eventually able to convince Shinji that what he does is merely escapism (a theme in the show), and as such Shinji is able to conclude that this new world is void and empty without the interactions of others, even if painful.
The ritual is undone, and all souls are released, and will eventually find themselves in human form again.
Attached: [NAOKI-Raws] 新世紀エヴァンゲリオン劇場版 -The End of Evangelion- 第26話 まごころを、君に (BDrip x264 DTS-HDMA5.1ch+2ch Sup Chap):00:29:57.png (1920x1080, 2.5M)