Operation Yashima begins at the stroke of midnight. Misato tells Shinji that he is being entrusted with all of the electricity in Japan, and wishes him luck. Through a series of connections, all of Japan’s energy is redirected to Mt. Futago. Each connection stage runs smoothly, with the cooling systems all working optimally. Unit-01 raises the firing hammer on the rifle. He begins to aim as the energy is transmitted to the positron rifle. At that moment, a high-energy buildup is detected within the Angel.
Shinji targets Ramiel’s core and fires, just as the Angel fires its energy beam. The two energy beams interfere with each other, sending them off course, missing both of their targets. Ramiel’s shot strikes the mountain behind Unit-01, overturning the control car the command crew is in.
At that moment, Ramiel’s drill pierces the final armored layer and penetrates into the GeoFront itself.
Shinji reloads the fuse for a second shot. As he waits for the gun barrel to cool, another energy buildup is detected within the target.
Ramiel fires directly on Unit-01, but its shot appears to be deflected.
Shinji looks up to see that Rei in Unit-00 has jumped in front of Unit-01, deflecting the shot with its shield.
Shinji awaits the target lining up with a frantic impatience while Unit-00′s shield begins to melt away. Once the target is in the center, Shinji fires, and the beam strikes the Angel through its core, destroying it.
Unit-00 collapses and Shinji calls out to Rei, while Ramiel’s drill falls silent.
Shinji has Unit-01 rip open the covering of the entry plug on Unit-00′s back. The plug is force ejected, and Shinji extracts it in Unit-01′s hand. He then gets out of his EVA and opens the hatch on the plug, bursting in to see if Rei is alright.
Rei lifts her head up, and on the verge of tears, Shinji tells her not to say that she has nothing else, and not to say farewell when leaving somewhere. He begins to cry, and Rei apologizes, not knowing what to do in a situation like this. With a mixture of relief and tears, Shinji suggests she should smile. Rei looks at Shinji, and sees in him a reflection of Gendo smiling. Rei relaxes from her tense posture, and smiles at Shinji for the first time.
(Events depicted in episode 6. A full timeline of the events depicted in Evangelion can be found here.)