This is book number 3 in the Neon Genesis Evangelion: ANIMA (Light Novel) series.
ARMAGEDDON, ALL OVER AGAIN
Severely wounded in battle with Armaros, Shinji struggles to shoulder the responsibility of being Earth’s savior yet again. Meanwhile, Asuka adjusts to her strange new body, and the clones Trois and Quatre continue their quest for their own identities. But their enemy wields the power of a god, and it’s going to take every single one of them working together to prevent a reprise of the Human Instrumentality Project.