Authors Notes: Chapter One was rushed. Chapter 2 should be better. Also I have omitted certain conversations, so you can watch the anime again to get the details. As I have no way to check the facts I have tried to make this chapter more like the show. Sorry if it still seems like it is lacking something.

Chapter 2: Crimson Smile

The silence was getting to Edward. He stared out the window and made a face as his brother was sitting like a statue and that bothered him. "Hey Al." Ed turned to his younger brother. The armor plated face looked down at the older brother, "Yes, Ed?"

Ed had to think quickly he just wanted another reassurance that Al was still in his body. "So, let's go over this mission again." He spoke quickly as he pulled a folder out of a satchel that Col. Mustang had given them.

"But, we have already gone over it five times brother." Al said looking weary at the folder that had shown signs of wear.

Ed ignored his brother as he began to read aloud, "We have learned of an Alchemist in a far away land called Japan. The targets name is Shinji Ikari age fourteen." He handed the picture of a brown haired blue eyed boy to Al who sighed and took the picture again. "Our mission," Ed continued, "is to watch over Shinji and make sure nothing happens to him."

Without warning the train lurched to a stop toppling Ed and Al out of their seat. When the train had come to a complete stop an announcement began, "We are sorry for the delay, but Tokyo-3 is under a state of emergency declared by NERV. At this time we are waiting for the emergency to be lifted. We apologize for the in convince."

Ed stood up slowly rubbing his head looking at the PA speaker. "State of Emergency?" He looked wide-eyed at the PA. "Ed, look!" Al pointed out the window to silver light, and floating in the light a cube turned on its side firing a beam of light at something that was still hidden behind a mountain. Then the beam started to sink down and then stopped.

"W-W-What in Hell was that?!?" Ed stammered looking both curious and frightened at the same time. "I don't know, but whatever it was, it was sure powerful." Al said in the same amazed voice staring out the window.

DING-DONG

"At this time the Tokyo-3 Express will now return to the last station. We apologize for this inconvenience." Spoke the female voice of the Train's conductor.

The train started to lurch backwards. Ed and Al looked at one another. Then back at the thing.

Obviously this is part of the danger that the Col. Had mentioned. Al and Ed both thought.

Xxx

Evangelion Unit 01 slammed down into the catapult floor. Misato looked anxious at Ritsuko and Maya.

"Pilot's life signs are negative!" Aboa yelled suddenly startling Misato.

Ritsuko turned toward the monitors, "Administer 10cc of adrenalin and give him a heart message!" She had barley finished when Aboa typed the commands into the terminal and Shinji then jerked on screen. "We are getting a pulse!" Confirmed the long haired tech. Misato stood on the elevator that would take her to the Eva cages. "I'm going to go meet him!" The lift started to descend.

Xxx

By the time Misato had arrived panting hard, at the railing near Eva Unit 01's cage Shinji's command chair was already out of the Entry Plug. Her heart stopped as she saw him. Blood was trailing out of his nose and he was pale. "Shinji!" She whispered her eyes wide.

Xxx

Shiguru finished giving his report. Misato sat at the desk thinking about the information that she had just been given. Her hands in front of her face in a Commander Ikari-like pose.

"Pilot's status?" Her eyes moved over to Maya who quickly replied, "Unit 01's pilot is stable and recovering well. We estimate he will regain consciences in less than 6 hours."

Misato's eyes closed momentarily, Thank God he is okay! She thought, and then turned to Ritsuko. "About how much power will it take to penetrate the Angel's AT Field?"
The bottle blonde stiffened, "As you know no weapon in our arsenal including our Proton cannon has the out put available. We estimate that it would take the combined power of all of Japan to do it." Then she removed her glasses and sighed, "The problem is we don't have a weapon able to generate that much power, nor does NERV have the resources to use if we did."

Misato smirked, "Ritsuko you have just solved the problem."

Xxx

Two hours later Captain Misato Katsuragi stood about 15 feet from Commander Ikari's desk as she finished outlining her plan to him he gave no response.

"And what do the Magi have to say on this?" Ikari's cold voice issued from behind his white gloves.

"They give the plan a 6 percent chance of success; it is the best we've been able to get." Misato smiled still standing still her eyes fixed on to the Commander's.

Come on you old Bastard! Misato thought.

"You have a go, Captain." He spoke.

She saluted him, "Thank you sir!" And she left the office.

"Only a six percent chance of success?" Fuitsky said, his hands behind his back still looking at the door that Misato just left through. Gendo nodded, then asked, "And what of our two guests?"

The older man looked up as if trying to remember something, "Last report put them on the number 2 Tokyo-3 Express. They would have arrived earlier but the Angel attack forced the train back to Okinawa station."

The Commander gave a slight smile.

Xxx

Several hours later. Shinji awoke, Another unfamiliar ceiling. He thought frowning then the door clicked open and Rei walked into the room wearing her wrinkled school uniform. He sat up and Rei looked down, "You might want to cover that." She spoke emotionlessly looking at Shinji's package. He looked down and gave a gasp pulling the blanket up over his belly as he sat up holding his knees.

"Sorry." He mumbled.

Either Rei didn't care or she was not about to give him the satisfaction that she liked what she saw. But tossed a package with a new Plug Suit onto his bed.

"I'm here to outline the mission." She said. Then opened a black date planner in one hand and explained the mission. Before she finished, "I don't want to Pilot it anymore!" Shinji spoke quickly his voice full of anger. He still did not look at Rei.

She regarded him quickly and turned to leave. "I'm sure Doctor Akagi can rewrite Eva 01's system. Eat before it gets cold." She left and Shinji sighed.

Xxx

At the temporary Eva docking station knelt down with their plugs ejected. The night air was crisp and the full moon cast a glow off the Eva's armor.

Shinji and Rei sat in their Plug Suits in the night air watching the lake between them and the target. Shinji looked over to Rei, "Why do you pilot the Eva?" Rei blinked not expecting the question she did not look at Shinji as she replied, "Because I am told to."

Shinji frowned at her. She seems so sad. He thought and a beep issued from his watch. They both stood up and walked to the ladders that would allow them access to their Entry Plugs. Before Shinji put his foot on the first rung Rei spoke, "I will protect you Ikari-kun." He looked back at Rei who was silhouetted by the full moon light she had already climbed up half way up the ladder but her head was turned to him. He saw her red eyes look at him and nodded. She is beautiful in this light. The thought struck him from nowhere. Then she spoke again, "Goodbye, Shinji."

And with that she closed the hatch to her Eva.

Xxx

"Okay Shinji everything is ready to go. Just position the target in the center and the computers will do the rest." Ritsuko's voice came from the speakers. Shinji took a deep breath of LCL, It still tastes like blood. He thought as he pushed a switch on his right control stick. A visor gracefully fitted over his eyes and the display showed the Angel magnified. He watched the charge indicator till it lit up green.

The HUD hummed then he pulled the trigger.

The Eva's finger pulled the trigger on the energy sniper rifle and all the power of Japan coursed through it and then a brilliant blue light emitted from the end of the barrel streaking toward the Angel. Before Shinji know what was happening a yellow beam of light shot out from the Angel and met the blue beam in the middle of the lake they twisted around each other and forced the beams to both miss their targets.

"SHINJI! YOUHAVE TO BUY TIME FOR THE RECHARGE!" Misato's panicked voice filled his plug and she barked out a "Roger!" As the purple Evangelion picked up the rifle and pulled the cables standing and moving 40 meters to the right as the Angel sent another beam of yellow light at him he froze eyes wide. Then a flash of yellow and grey filled his vision and the beam impacted with the make-shift shield of Unit 00. "Rei!" Shinji bellowed then he brought up the rifle again pulling the hammer he pulled the helmet back over his face and lined up the shot.

Come, on! COME, ON CHARGE ALREADY! His mind shouted at the gun. The shield melted away then Eva 00 opened its arms spread eagle protecting Unit 01 as a beeping noise filled his ears he pulled the trigger.

A lance of blue light shot at the Angel and ran it through. The beam stopped, and something inside of the Angel exploded. But Shinji didn't care as he threw down the rifle and pulled Unit 00 up into a sitting position he wrenched off the armor cover and the Entry Plug ejected. When it was fully out the orange steam of LCL discharged out of the plug's emergency relief vents and ignoring the feeling of hot metal the Unit 01's nerves feed his CNS. He laid the plug on the ground then ejected his own Plug and slid and sprinted down his Eva to the hatch of Rei's.

He grabbed the handles of the hatch and started to turn them. His suit's hands started to smoke as the hot handles burned into the Plug Suit. With a sick wrench that took all his might, the door opened and steam poured out. He didn't care he ducked inside the plug shouting, "Ayanami! Ayanami!" Then he saw her laying there he waded up to her and shook her once she stirred and then weakly opened her eyes to see him looking at her his brown eyes full of tears then she got a flash of the Commander from when her Eva went berserk in the test cage. She sat up her body protesting at first. She didn't understand why he was crying, "Why are you crying?" She voiced.

"I'm not crying you idiot! I'm happy to see that you are alright!" He smiled at her. She kept her face a blank mask.

"I-I'm sorry. I do not know what to do." She stated looked down cast at the control board.

"How about smiling?" Shinji spoke warmly looking at her.

Rei didn't know why but she looked up at Shinji then happiness filled her as he spoke again.

"Rei, don't say Goodbye when you go off to a mission. It's just too sad." He said still smiling.

Then she tilted her head to the side and gave Shinji a warm smile.

PS: That was out of order I know. Sorry again. I promise chapter 3 will be much better.