This was Evangelion: 3.0+1.0 —but not the one you knew. In this thread, the 1.0 (the pristine, blue-skied beginning) and the 3.0 (the broken, crimson ruin) were not sequels. They were simultaneous.
At the center of the collapsing worlds, Shinji found the true Instrumentality: not the merger of souls, but the separation of timelines . Gendo had been holding them together with sheer will, terrified that if the two versions of his son met, one would forgive him and the other would hate him—and he couldn't bear either.
Behind the door, Gendo Ikari waited. Not the calculating monster of either timeline, but a man caught between them: his left hand cradling a photograph of Yui smiling, his right hand already fused to the trigger of the Impact system.
He took a step forward anyway.
Behind him, the Wunder was just a boat on the horizon. In front of him, Tokyo-3 was rebuilding—not as a fortress, but as a home.
The white-haired Rei simply vanished, leaving behind a single pair of glasses that had never belonged to her.
He didn't choose. He walked forward, pressed his young hand to his father's fused trigger-hand, and pressed his scarred hand to the photograph of Yui.
"You have to choose," Kaworu said, his AT Field flickering like a candle. "The pure boy who never failed. Or the broken man who never stopped failing. One timeline survives. The other evaporates."
"Two truths," Kaworu whispered, leading him to a door that hadn't been there a second ago. "The Near-Third Impact you stopped as 1.0 . And the Near-Third Impact you caused as 3.0 . They're both real. And both are collapsing into each other."
"No," he said.
"You blinked," Kaworu said, his smile gentle but his eyes old. "And the world ended twice without you."
Shinji Ikari didn't remember the 14-year gap. To him, one moment he was pulling the Spear of Cassius from Unit-01's core, the next he was staring at a sky the color of old blood, standing beside a man named Kaworu Nagisa on the cracked deck of the Wunder .