Episode:06

"Decisive Battle in Tokyo-3" is the sixth episode of Neon Genesis Evangelion.

Overview
The Angel Ramiel is boring down through the upper layers of Tokyo-3 to reach NERV Headquarters in the GeoFront below. Possessing a strong beam attack and the strongest A.T. Field ever observed, a direct assault by an Evangelion would meet with failure. A plan ("Operation Yashima") is devised in which Shinji in Unit-01 will use an advanced prototype positron rifle to shoot Ramiel from outside its target zone, which must use the entire electrical output of Japan in order to operate, while Rei in Unit-00 shields Unit-01. The battle ended with Ramiel killed, and Rei smiling at Shinji for the first time.

Synopsis
This episode resumes the end of episode 05; Shinji is launched in Unit-01, but the Angel sensed the Eva and shot it before the removal of the restraints. Unit-01 is recovered and Shinji is rescued and hospitalized. The Angel then settles over NERV Headquarters and began to drill into the GeoFront's armor plating. NERV estimates the Angel will reach HQ within few hours, and launches dummy attacks to analyze the Angel, and the results were that the Angel attacks any hostile inside a certain range and maintain a very powerful A.T. Field, making the Angel "a flying fortress".

While Shinji is recovering, Misato comes up with a reckless plan: to destroy Ramiel with a positron beam rifle, fired from outside Ramiel's attack zone. In order for this plan to work, the rifle must be able to withstand a tremendous amount of electric energy; for it is determined that they will need the power from all of Japan to pierce Ramiel's A.T. Field. Gendo approves this plan, and Misato requisitions a huge Positron rifle from the JSSDF's labs. Rei's part in the operation is to shield Shinji, who will be the shooter in Unit-01. For this purpose, they built her a shield that will stand up to Ramiel's beam for 17 seconds. The only problem left is whether Shinji will pilot Unit-01.

Shinji has regained consciousness, and Rei enters his hospital room to brief him on the plan's schedule. When he says that he does not want to pilot the Evangelion, she replies she will pilot it instead and then leaves the room saying goodbye.

Several of Shinji's classmates, including Toji and Kensuke gather to watch the Evangelions launch wishing them good luck. Back to Tokyo-3, Ramiel is still drilling to reach the GeoFront with less than 4 hours left, while the preparation for on Mt. Futago is still in process.

Misato and Ritsuko explain to Shinji and Rei their rules and the weapons work. While the two pilots are preparing for the mission, Rei reassures Shinji that she will protect him. When he asks her why she pilots, Rei tells Shinji it's because of the bond she has with others, and because she has nothing else in her life. She then bids him farewell.

The time now is midnight, and "Operation Yashima" has been commenced. As the countdown for shooting has began, Ramiel starts to charge to attack the Evangelion and shoots toward it along with the rifle's shot, resulting in the collision of the two beams and the two shot have missed. Ramiel's drill has breached all armor layers and reached the GeoFront while charging up for a second attack, which it can fire at Shinji before he can prepare his positron rifle for a second shot. Rei, in Evangelion Unit-00 steps in and shield Unit-01 from Ramiel's beam, but both the shield and Unit-00 sustain severe damage in the process. Shinji fires his second shot, which pierces the angel and kills it, stopping the drill. Shinji force ejects Unit-00's entry plug and opens the hatch. Rei is unharmed and unfazed. Shinji cries telling her not to say "I have nothing else", or say goodbye when going on a mission. When a confused Rei says she doesn't know what to feel at such time, Shinji replies, "why not smile?". Remembering Gendo's smile, Rei smiles at Shinji.

Quotes
Rei: "Why do you say that?" "...You won't die, because I'll protect you." Rei: "Because I have nothing else" Shinji: "What do you mean, "you have nothing else"?" Rei: "It's time. Let's go... Goodbye". Shinji: "Ayanami! Are you all right?! Ayanami!" (Rei opens her eyes and looks at Shinji) Shinji: (starting to cry) "Don't say... Don't say that you have nothing else. Don't say goodbye when you leave on a mission, it's too sad." Rei: "Why are you crying?..." "...I'm very sorry, I don't know what to do at a time like this." Shinji: (crying) "You can just smile." (Rei looks completely confused, then remembers Gendo Ikari smiling, and smiles at Shinji for the first time.)
 * Shinji (while Rei is still changing): "We might die doing this"
 * Shinji (after he asked Rei why she pilots the Evangelion): "You're very strong, Ayanami."
 * (Shinji breaks open Unit-00's Entry Plug)