This is the complete scenario of the first part of the End of Evangelion movie. The first 2/3 of it could also be seen in the second part of the previous movie: Death and Rebirth. The End of Evangelion movie also replaces episode #25 and 26 of the TV series, found in the Genesis 0:13 video. The "Air" part that is written here replaces episode #25. I won't do the Death and Rebirth movie, mainly because the first part is a resume of the first 24 TV episodes, and the second part can be seen here.

Please note that there may be some very minor differences between the text spoken by the characters in the movie and this "script". Background speach occuring while a main character is speaking may not always be written. Also note that some phrases may not be translated to perfection. You will find nonetheless that this guide to End of Evangelion: Air, is very complete and that no story elements, even minor ones, are left out. I also assume you know a little about Evangelion since that movie cannot really be understood by people who havn't seen the TV series.

Finally, note that because English is not my primary language, I am pretty sure that some errors will go into the text. Try to overlook them :-)

End of Evangelion: Air

The movie open with Shinji standing in front of the now ruined Tokyo-03 city. A lake has replaced what was once a proud city. Bits of scraps falls in the lake here and there from crippled electrical poles and such...

We now find Shinji in Asuka's hospital room. Asuka is lying on a bed.

Shinji: Help me! Hey, help me Asuka! Make a fool of me like you always do!
Shinji begins to shake Asuka, waiting for a response. Asuka, who was lying on her side, falls on her back. Shinji is surprised when he sees Asuka's breasts now revealed to him. After that, pictures of the walls and doors can be seen while we hear Shinji masturbating. We then see Shinji's hand full of sperm.
Shinji: I'm helpless.

Nerv's command center: The usual command center near the Magi system seen through the series.

Aoba: Nerv personnel is not allowed out. We're still at first stage emergency.
Maya: Wasn't that boy the last?
Makoto: I wonder what will happen to the Evas?
Maya: Ritsuko-sempai isn't even here.
Aoba: I hear that Nerv is going to be dismantled.
Makoto: I guess we have to be patient until instrumentality.

We now see Misato in her car with her forearms on the steering wheel, parked alongside a road outside. It is getting dark.

Misato (to herself): The instrumentality is the last stage of mankind: artificial evolution. That's why the committee wants to use neither Adam or Nerv, but Eva... That's what Kaji said...

Seele council (the usual "voice only" circle in the dark also seen a lot during the series):

Keele (Seele voice #1): The time has come. We've lost the spear of Longinuss. We cannot proceed with Lilith, but hopes to proceed with Eva, child of Lilith.

We see a picture of the lance of longinuss, planted in the moon.(Blooper note: wasn't it supposed to be in lunar orbit? Looks like they forgot, but it's unimportant at this point, isn't it?)
Gendou: That's different from Seele's scenario.
Fuyutsuki: The value of mankind was to produce Eva.
Gendou: We should live in a new and different world. That is the reason for the Eva series.
Seele #9: It's not necessary to alter human form to board Noah's ark named Eva.
Seele #12: It's just a formality. This is for the rebirth of the last stage of mankind.
Unknown Seele member voice: God made every living creature unite at death and become one.
Gendou: Death creates nothing
Keele: I'll give death to all of you. The "voice only" panels of the committee fades away, only Gendou and Fuyutsuki are left.
Fuyutsuki: Mankind's greatest ability is to survive against all hardship to survive. It's why it places his hopes on Eva.

Rei's apartment Rei wakes up, looks at the sky, then leaves her apartment. Gendou's glasses that she kept are found lying on the floor, smashed and broken (more than before).

Shinji is seen lying on the floor with his usual cassette player. No music can be heard, the indicator of the player is stuck on 00:00 and indicate "low batteries".

Brief view of the outside. It's morning, with fog.

We now see Misato inside a refrigerated computer room. Lying on the ground, with her head against a wall. She is typing on a portable computer and is hacking in the system.

Misato (to herself): So that's the meaning of the second impact. A clanking noise can be heard
Misato (to herself): They found me! no, it's starting.
A panic type of music starts to accentuate the excitation.

Nerv's command center:

Fuyutsuki: Open a line to the satellite. Situation?
Intercom voice: Communication system down.
Fuyutsuki: Is the enemy's target the Magi?
Aoba: Receiving data. Their goal is hacking into Magi!
Fuyutsuki: As I thought. Is the ennemy Magi type 2?
Aoba: No at least type 5! Invaders are from Germany, China and America!
We see a diagram on the screen of five magi hacking into Nerv's Magi.
Fuyutsuki: Seele seems to be using full force. 1 against 5, it's hopeless.
Intercomm voice: Firewall down!
Makoto: Closing database. It's not working!
Maya: Outer front and auxiliary pathways won't work either!
Gendou can be seen in the background keeping his cool with his hands on his mouth, elbows on his desk.
Fuyutsuki (to himself): This is bad. Losing the Magi means losing the main office.
The panic music stops.

We now see Ritsuko's dark cell: An unknown (unimportant) character open the cell door. Ritsuko sitting on something (bench or chair, we can't see) with her head low, elbows on her knees.

Ritsuko: It's about Magi's defense isn't it?
(Unkown): Yes, ask Ibuki for more details.
Ritsuko (to herself): He'll even use the woman he dumped. How selfish.

We see Misato walking at a determined paced in a corridor speaking in a portable transmitter/receiver.

Makoto (via radio, speaks about an 803 special command. Just really unintelligible chatter. Here's the ending of the conversation, the only part where we can understand something): They are transferring control to the japanese governement.

The scene changes to the command center, the conversation between Makoto and Misato continues.

Makoto: They're hacking into Magi. It's under control.
Maya: This is Ibuki speaking. Dr. Akagi has started working on the defense. Misato arrives in the control center
Misato: Ritsuko?

Inside of Magi Caspar: Ritsuko is lying on her back, near Caspar's brain. "Scars" from the previous Caspar "surgery" of TV episode #13 can be seen on the "brain's" protective shell. The designers notes are still lying everywhere.

Ritsuko (to herself): Am I foolish? There is no logic between man and woman. Ain't I right mother?

Shift back to command center: Misato drinking coffee

Misato: How long do we have to wait?
Makoto: It's on time. Dr. Akagi's ability incredible!
Fuyutsuki (to Gendou in the back): This attack is pre-emptive. The ennemy's objective is probably to take the main facility and both Evas.
Gendou: Yes, we have Lilith and Adam too.

Back inside Caspar: Ristuko leaves Caspar

Ritsuko: See you later, mother.

Seele's council:

Unknow Seele voice: Ikari has set the 666 protection. It's not easy to break.
Another unknown Seele voice: We have no choice but to cancel the occupation of the Magi.
Keele: I've decided to occupy the main facility directly.

We now see various view of the outside, above the geo-front. Troopers with dark blue to black combat uniforms can be seen in the bushes.

Unknown trooper: It's started, move out as scheduled.
We see at least 50 troopers rising to their feet (the scene shows that they're is a lot more than that). Planes are arriving above the Tokyo-3 lake (where the city was). Tanks are arriving by road, aligning themsleves in row, and starts shooting.

Nerv's command center:

Intercom voice: Radar site #8 to 17 cut off. Screens go white, others starts malfunctioning.
Another intercom voice: Troops invading defense line.
Fuyutsuki (to Gendou): As I predicted, our last ennemy is human.
Gendou: prepare for combat stage one.
Maya: Prepare for combat? (in a softer voice) But the enemy is human like us.
Makoto: I hope they think the same.

Outside view above ground: Missiles are fired, explosions results.

Railway station: A Nerv guard is killed, backstabbed by a trooper. The doors to the railway starts to open, revealing around 30 troopers behind (more can be guessed behind the first row). As the railway door open, the alarm system goes on.

Two guards are standing near a truck in a garage:

Guard (in a radio transmitter): What's wrong? Hello?
We hear two heavy gun shot and two big holes being punched in the truck. After a second or two, the truck explodes, the blast taking out the two guards.

A "panic" kind of music start. The scene returns to the railway station that is now open. Lots and lots of troopers get inside the facility. The dead backstabbed guard is just walked in his blood by the running troopers.

Nerv's command center:

Intercom voice: Fire in the warehouse
Another intercom voice: Tunnel has been sealed.
Yet another intercom voice: Invaders in west building.
Misato (yelling over the intercom from the command center): The decoy is entering from the west building, if their goal is the Evas, they'll attack the pilots!
Misato (in Makoto's hear): Have Shinji prepared and ready in Eva-01.
Misato (at all technicians): Where's Asuka?
Aoba: In room 303.
We see an image on a monitor of Asuka in her hospital bed, looking at nothing (well the ceiling, but she looks more like a vegetable), not moving an inch.
Misato: Take her to Eva-02!
Maya: But she's not fully synchronized with the Eva!
Misato: She'll be killed if she stays there. It's better to hide her in Eva-02 to protect her.
Misato (to Makoto): After that,; move EVA-02 in the underground warehouse.
Misato (to every technicians): Where's Rei?
Aoba: We lost her, we don't know where she is!
Misato: Try to locate her, she may get killed. Hurry!
The panic music stops.

Rei is seen floating in her usual tube (gene tank), deep below Nerv's installation.

Another panic kind of music starts We see the launching pad of Eva-02. Eva-02 is launched the usual fashion via a vertical lift.

Back to the command center:

Misato: Launch Eva-01 and position it in the geofront ligne.
Aoba: Can't, the pilot is still...
We see, on a black and white monitor, Shinji crouched in fetal position, his head between his crossed arm on his knees. He seems to be hiding underneath a stairway.
Misato (looking at Shinji via the monitor): What the?

Various pictures of gates closing here and there in Nerv's facility. Comm chatter can be heard in background.

Command Center:

Aoba: Route 3 destroyed and warehouse #2 invaded.
Fuyutsuki (to Gendou): A complete take over is just a matter of time. Gendou raises from his chair
Gendou: Fuyutsuki, take care of the rest.
Fuyutsuki (looking at the main screen, not at Gendou): I know, give my regards to Yui. Gendou leave the command center.

Explosions at various places in Nerv facility can be seen. Scenes that can be seen:

• Troopers firing submachine guns and rifles in corridors.
• Troopers firing bazookas in a parking lot.
• Flying vehicules descending an elevator shaft and shooting in secondary horizontal passageways that result in explosions in them.
• Troopers running with fire in the background.

Command center:

Intercom voice: No answer from group two.
Another intercom voice: Communication office 77 cut.
Yet another intercom voice: Rail 52 has been destroyed.
Makoto: They must have had something wrong. They're very cruel.
Misato (to herself): It's not suprising this is happening, no one is trained to kill.

Panic music continues, but it gets louder. A girl in Nerv uniform is shot while trying to help a dead Nerv operative in a corridor.

Corridors shot and destroyed. We see various dead Nerv operatives bodies everywhere in their own blood. Another man in Nerv uniform is shot in the back while he was trying to run.

We now see troopers in a corridor:

Trooper (on a radio transmitter): Cut the red cable.
Another trooper in the back is seen firing inside a cable access panel.

We now see other troopers in front of a doorway a semi-portable flamethrower pointing towards it. They fire the flamethrower in the other room. Screams can be heard in the background. They fire the flamethrower a second time. The screams are heard again.

We see other troopers running among dead bodies.

Command center:

Makoto: Invader in B-block, impossible to stop.
Aoba: S-block taken, all were shot in the main bypass.
Misato: Seal off level 3. All combat troops are to be receded. Pipes and routes to section 803 will be filled with Bakelite.

Bakelite starts being injected in various corridors, flooding passegeways. (Bakelite seems to be the red liquid that is used to protect the Evas when they are inactive).

Intercom voice: Starting bakelite injection.

Command center:

Misato: I hope this helps for a while.
Makoto: Captain Katsuragi. Route 47 destroyed. Group 3 unable to proceed forward. If this continues, Shinji's life will...
The panic music stops

Shinji can be seen, still in fetal position, underneath the stairway.

Misato (in the background, she's not really there): Tell all non-combative troops to avoid close-ranged combat if possible.

Command center: Misato is seen readying her pistol.

Misato: Our opponents are pros. If they can't get back to dogma, tell them to surrender.
Misato (in Makoto's ear): I'm sorry, look after things here.

Above the surface, planes starts shooting. Troopers are seen with the Tokyo-3 lake in background.

Trooper: It's taking hours longer than expected.
Another trooper: They are no easy jobs.

Command center: Misato is no longer there. Makoto is taking a gun in a drawer.

Makoto: It's hopeless, our system isn't designed to allow us to attack troops.

Aoba is readying a machine gun.

Aoba: All we can do is scare them. I wonder if the budget reduction were planned from the start.
Makoto: Maybe...

We see (and hear) an explosion. The two technicians are shaken. Troopers with riot shields enter the command center, on the lowest level and starts shooting. Aoba gives a gun to Maya, who is hiding underneath a console.

Aoba: here, unlock it.
Maya: I... I can't shoot.
Aoba: You did it many times in training!
Maya: But they weren't at people!
Aoba: Fool! Shoot or they'll kill you.

Maya seems terrified.

We now see the still naked Rei Ayanami looking at what remains of her destroyed counterparts. Arms, limbs and various parts of the anatomy of her doubles can still be seen floating in the tank. Gendou arrives.

Gendou: As I thought, you're here.

Rei turns her head to look at him, slowly, no emotions showing.

Gendou: The promised time has come, let's go.

Corridor with dead Nerv personel lying in the floor. We hear radio messages,

Trooper (via radio): From level 2, Magi hasn't been found yet.
Another trooper (via radio): Use heat treatment, it's tricky, still investigating.

At the end of the corridor, a man in Nerv clothing is seen on his knees, hands in the air, surrendering. He gets hit by two shots: head and torso. The trooper who killed him appears and put his left foot on the dead man, and shoots twice more in him with a pistol.

We return to Shinji below the stairs. 3 troopers are around him.

Trooper (on radio): Found the third, will erase him.
Same trooper (to Shinji): Don't hate me boy. Bang!

A trooper falls down, blood going out of it's head. We hear running footsteps. We see Misato, firing her pistol like a maniac at a second trooper who dies shortly after. She rams the third trooper and placate him against the wall, her gun below his chin.

Misato: Don't hate me! Bang! She kills him.
Misato: Let's go, to Eva-01

Shinji doesn't move during all that. he only recoils further in his fetal position, not looking. His head his hidden inside is arms.

We now find Misato and Shinji hidden between two cars in a parking lot. Misato use a dead trooper's radio to hear comm chatter.

Misato: Not good, they are destroying physical routes between Shinji and Eva-01. Let's go, Shinji. Shinji has resumed his fetal position, sitting on the floor of the parking lot.
Misato: Decide if you want to run or go to Eva. Otherwise you'll die without having accomplished anything.
Shinji (to himself, but Misato can hear): Help me, Asuka, help me...
Misato: Relying on women, running away and deception. Indecision is the worst. Stand up!
Shinji: No! I don't want to do anything. I want to die.
Misato: Don't waste your life doing nothing! Spoiled kid!

Command center:

Dead nerv bodies on the lower level. The shooting continues. Technicians on various level (near the Magi, or the primary command console) shoot back.

Fuyutsuki (in a red phone): I don't care! Give priority to dogma!

He hangs up. Maya is hanging desperately to a clipboard, still under the console.
Makoto: They destroyed everything. But they won't do that here...
Aoba: They'll do it all at once. They probably know the Magi is below us.
Makoto: They may want it taken without scratches.
Aoba: Our anti-biological/chemical system is down, if they use those wespons, we'll be in trouble.
Makoto: An N2 bomb as well. Maya seems scared to death.

Outside, a plane passes over the Tokyo-3 lake. It launch a bomb. Seconds later, it explodes. The N2 bomb opens up the surface of the geo-front.

Command center: Everything is shaking, result from the explosion.
Aoba: Oh, God!
Makoto: They're not using common sense!
Fuyutsuki: Fools!

Inside the geo front, but outside Nerv's HQ: We see some 200 (I didn't really count them, this is approximately), white lines falling from the sky. When they touch the ground, they explodes. (Most likely missiles).

Command center: Maya is covering her ears, the room is shaken again.

Maya: Why do they want Eva so much?!

We now see Misato driving her car with Shinji.

Misato (to Shinji): They are awaiting the third impact with the Evas, not the angels.

We see images of the discarded Eva prototypes we saw in the TV serie.

Misato: The 2nd impact was pre-set by human beings. The damage was minimized by turning Adam into an egg before the angels awakened.

A flashing image of Adam. The giant of light, looking like an illuminated shadow of an Eva.

Misato: Shinji, we humans and Adam come from Lilith, the source of all living creatures. We're the 18th angel. The others were possibilities that had non-human form.
Misato: We rejected and neglected each other even though we were human, it's a sad existence.
Misato: Shinji... Destroy all of the Eva series. It's the only way for us to survive.

Office of Nagano prefecture, Tokyo-02. It's a typical bureau, except it's really huge, lots of huge windows, and a big (let's say enormous) pendulum of a clock is swinging left and right across the room. 2 persons are present, one of them sitting behind the desk. (They are very far, so we can't see them very well).

Unknown character: It's confirmed, the bombing occured 3 minutes ago.
Prime Minister: The goal of the human instrumentality plan advanced by Nerv was to incur the third impact. This would mean the end of the human race. It's not acceptable.
Unknown character: Only we humans can hate each other among all creatures.
Prime Minister: The remaining job is cleaning up Nerv's office.

Outside Nerv's HQ Troopers are speaking among radio.

Radio chatter: Dogma level 3 under control.
Another man in radio chatter: "Purple" under control.
Trooper (who holds the radio): What about "red"?
Radio voice: It's been found underwater, depth 702 in Shite lake. It's unknown if the pilot is still alive.

We see Asuka, that assumed a fetal position inside unit-02's entry plug. She wears her red plug suit.

Asuka (to herself): I'm alive.

Outside, tanks and such are shooting something inside the lake.

Underwater, we see depth charges falling towards Eva unit-02. They explodes near it. One of them "bouces" on it's head before explosing.

Inside Unit-02's entry plug: The plug is shaken as the charges explodes. Asuka takes her head with her arms and seems to groan. Then silence.

Asuka (to herself, in a voice that can barely be heard and that gets louder): I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! I don't want to die! In parallel to Asuka's conversation to herself, we can hear phrases like:
(see below for who's speaking): Live on! Don't die! Live true! I won't let you die! (with some repetitions).

We then see various pictures. Asuka as a child, the shadow of Asuka's mother, then Asuka reaching and touching the hands of her mother. During those brief sequence, Asuka speaks with a little child's voice:

Asuka: Mama, you're here...
Asuka: MAMA!

We then see Eva unit-02's head. It's four eyes are opening up...

(A note from me*the author*: For those who didn't understand that scene, it is more proof that the "souls" of the Eva pilot's mothers are "stuck" inside the Evas. In the TV serie, we see Shinji finding his mother in a similar fashion. For those who like to make relations and suppositions, remember that all of Shinji's classmates are candidates for piloting Evas and that none of them seem to have a mother alive (as seen in the TV serie). Kind of scary no? Also remember that Asuka lost synchro with her Eva when she thought about her past life, primarily about her mother. Now, she seems to accept her again, looking more of a young child than ever...)