Yes, Shinji tried to save Rei and ended up accidentally fusing the angels core with the Eva 01 and Lilith's soul (not that anyone told him that would happen or tried to stop him or told him not to, Misato even encouraged him to do it). But the impact was stopped by Kaworu with the Spear of Cassius.
It was the 12th angel possessing the Mark 6.0 , and Rei's clones fusing with Lilith's body that caused the third impact killing all those people, and Misato knew this since it was her who ordered to take the Spear of Cassius from the Eva 01 to impale this new fusion.
So why is everyone acting like it was Shinji and not Gendo/Rei/12th Angel? Shinji wasn't even awake when that happened!!!!



