Makoto was going about his day at NERV after the Third Child's return. "That girl. She has my last name, yet I don't have eyes like hers and I sure don't have her x-ray vision. I mean, I need glasses to see, but we're from different worlds, so I guess it's just a coincidence."

Like most of the NERV staff, he was having a hard time handling this whole 'humans can use the A.T. Field and gain superpowers' thing and the 'people from another universe' thing.

But, little did he know, things were about to get weirder, for five seconds later, Gendo's true plans and the proof of it started playing on every screen in Tokyo-3.

As they found out later, this was the doing the shadow clones of Shinji and Misato.

With his plans revealed, the Japanese Strategic Self-Defense Force appeared out of nowhere and started attacking the place as Gendo quickly went to further his plans.

Now, this army soon found themselves being beaten by the Leaf gang.

Karin simply used a Chakra Chain with a Rasengan on the end to knock them over and send them flying into the walls.

Kiba used his clan's newly-rediscovered jutsu to turn into a werewolf which made the special forces run away, screaming for their mamas. Most of NERV did the same thing.

The J.S.S.D.F tried to fire on Naruto, only for him to raise his hand, making their bullets stop in mid-air.

Naruto looked at them and said, "Is this really the best Shinji's world has?" With a flick of his wrist, the bullets went back where they came from, taking down an army like it was no trouble at all, but, let's face it, guns verses Rinnegan. The bad guys never had a chance to start with.

Shino, who had forgotten to introduce himself last chapter, rolled up his sleeves so that the army could see the bugs fly out of his skin at them and the bugs exploded on contact. "Insect Bomb jutsu. I love it," was all Shino said and that was the most emotion that he had ever shown in his life.

Down at the Eva cages…

Asuka, Toji, Hikari and Kensuke were looking at Eva's 00, 01, 02, 03 and 04 which looked like a silver version of 03 and 05.

The four of them had thought the Eva's were mankind's saviors, but they were just their mother's coffins.

Shinji appeared. "Guys, I know that a lot is going on, but this is the truth. I promise. When the last of the Angels are done for, all three of them, I'll find a way to free our mothers' souls from these things, but, right now, get out of here."

Asuka crossed her arms. "Why should we, freak?"

Shinji crossed his arms as purple chakra stormed around him. "Because I can use the A.T. Field or, as it's called back in Naruto's world, chakra, outside of an Eva. Plus, I know how to fight. All you've done is speak about how great you are, Asuka. Well, news flash. You're the worse pilot around. I was the best. You always put me down, saying I was weak. Well, I think it's funny that the person you put down all this time was the one you wanted to be."

Shinji made four shadow clones, each of whom greeted one of his fellow pilots and turned on their Mangekyo Sharingan. The clones all used Kotoamatsukami on them, giving them basic Shinobi skills… and rewriting Asuka's personality, the later of which was long overdue.

His friends passed out and the clones carried them off.

Shinji sighed. "If only I could have changed Asuka that easily sooner, but I'd best go meet Misato, Rei and Sai down below were Lilith is."

He then dashed off, stopping only to watch Yamato use Wood Release to restrain Ritsuko and some more of the J.S.S.D.F.

Shinji looked at the bottle blonde. "How can someone who reminds you so much of Lady Tsunade be so evil as to work With Gendo on ending the human race and to sleep with him? She's fucking crazy!"

Down below, Gendo was walking with the embryo of Adam fused into his right hand with a clone of Rei that was fresh out of the test tube and dressed in only a white dress.

In front of Lilith stood the real Rei, Sai and the now-teenaged Misato.

The real Rei looked at second Rei. "Sister, do not listen to our creator. He speaks of lies. He only wants to use you. Trust me. I know."

Gendo looked at the girl. "I don't know how the brat was able to turn you against me, my little doll, but it matters not. I have your replacement."

Sai looked between his Rei and the second one. "At a time like this, is it wrong that I enjoy the sight of two Rei?"

Misato smacked him on the head. "YES IT IS!"

Gendo pulled out a gun with his left hand. "Do you think I'm scared of children?"

Another Sai behind Gendo appeared and quickly summoned an Ink Lion. "You should be."

The lion made from chakra ink attacked Gendo and ate his right hand, removing Adam from the world.

The second Sai turned into ink, as did his lion. The real Sai pulled out his tantō as his Rei blew Ice Release chakra at Gendo, binding him to the ground in ice so that only his head was free.

The second and newly-born Rei ii looked around, not understanding any of this.

Sai squatted down so that his tantō was at Gendo's forehead. "What you were doing is now public knowledge as well as everything else that was going on here. You are done for, and Shinji also met his mother in Eva-01. She made him promise to stop you at all costs. The Angels will fail. The world will know how to use the A.T Field. Any last words?"

Gendo shivered as he said, "I doesn't matter. I planned in case this would happen when that Itachi man showed up."

Rei, Sai and Misato gasped. Rei II looked at them and finally spoke. "Do I even want to know what's going on here?"

Sai quickly thrust his tantō into Gendo's head, killing him as Shinji showed up. "No. You don't, second Angel."

Misato jumped into Shinji's arms as she said, "ITACHI IS HERE AND HE AND GENDO MADE SOME KIND OF DEAL!"

Shinji's eyes widened as he said, "Oh, shit! Looks like this isn't the quick end we wanted."

Behind them, Lilith vanished.

Rei spoke. "I think I know what the deal was now."

Meanwhile, Hinata had made her way to Gendo's office.

She quickly used the Gentle Fist to break the lock and headed in.

As plain as day on his desk was a file that was black with red clouds on it.

The formerly-shy girl picked it up and her eyes widened as she read it. "He agreed to hand over Lilith if he dies. What do the Akatsuki want with Lilith?"

Her pet kitsune Kyū popped out of her jacket and yipped.

Gendo was gone. The world knew his plans, about there being another universe where humans learned how to use the A.T. Field and what could be done with it and the Leaf Village gang had only been there for an hour.

Meanwhile, in the command center, Maya was with Kurenai.

Kurenai grabbed a shaking Maya's shoulders. "You're a solider. You need to stop shaking. You're the highest ranking officer left. You need to lead."

Maya was quivering. "But I'm not a trained fighter. I'm just the computer girl. I wasn't trained for this."

Kurenai crossed her arms. "You think I was trained to deal with this level of bull ship either? But I'm not shaking like a leaf. You just need to order everyone out."

Maya hit a button on the controls to give an order to the base and she yelled out. "This is Maya Ibuki, the highest ranking officer on duty. Our leader was a liar. Our former Head Scientist was a dumbass who only got her job by sleeping with Gendo, so head out, go home and hold your families close. This day is over. The kids from that other world have got things under control."

Maya then turned around and fell down on her knees, hyper ventilating. The J.S.S.D.F had been beaten by kids. NERV was used to bring the end of mankind instead of save it and now she was alone in a room with a beautiful red-eyed woman from another universe.

This was one hell of a day.

Back with Shinji's group…

Rei was welcoming her sister Rei II to the family as they entered the main floor of NERV. Shinji only said one thing. "I hope showing the world that humans can use the A.T. Field was a good idea."

Misato grabbed onto his arm and gave him a peck on the cheek. "I'm sure it was, Shinji. After all, now you don't have to hide anything."

Sai looked back at him. "Besides, if we get in any trouble, we can use the Clone jutsu to bring it to an end."

Kimimaro walked up to them, only saying, "But now, let's find a place to rest for the night. After all, this day is done."

Everyone left NERV. On the streets, police were gathering, arresting the J.S.S.D.F., Ritsuko and just looking at Naruto's freaky eyes.

Misato ran up to Ritsuko who was now in the back of a cop car. "If only you would have used your mind for good, Ritsuko, then may be you wouldn't be here and you would be young again, too."

Ritsuko looked at Shinji and his Mangekyō Sharingan eyes and said, "Well, when I thought it was a good idea. I never thought I would have to factor in the boy being a bigger monster than his father in some ways."

Misato crossed her arms. "You haven't seen how much of a monster Shinji can be yet, Hang, but right now, we're all going to go find a place to figure out what to do with two Rei's. Now, bye. Also, my Shinji can make an army of clones and thanks to an incident involving a shower I can tell you he is twice the man Koji is. "

Misato ran off, leaving Ritsuko blushing and filled with envy. "I made the wrong choice when I did everything, didn't I?"

To be continued…

The NERV Arc starts off big, everyone. Hope you all liked it and the many changes and shocking twists that await from this point on.

Also, please vote on the new 'best battle' poll on my profile to vote on which battle in the first half of the story is the fan favorite.