This story is set in a time when Touji hasn’t become the fourth child yet and Asuka has been in Japan for quite a while. It’s just a story that doesn’t really have to do with what happens in the series.
Okay, so I'm not familiar with the whole activation procedure, so correct me if I'm wrong, okay?

Chapter 1

Shinji grasped the butterfly handles of his EVA tightly, breathing in deeply, his eyes closed. This is it! This is a battle! At this rate, I’m going to lose before I even start to fight.
"Shinji, what’s the matter with you?!" Asuka yelled through the speaker. Her face appeared through the small viewscreen, contorted with anger.
"Shinji, just aim and fire!" Misato said, her image overlapping Asuka’s. Shinji nodded, opening his eyes and staring at the angel. At his height, he could see it in full length, up close. It was hideously ugly, like a purple serpent covered in jelly. Green jelly that dripped to the ground every now and then. It reached out at the EVA with its scale covered tentacles, hissing with electricity.
Shinji clenched his teeth, aimed at the Angel’s core and pressed the trigger. There was no way he was going to let this Angel touch him. Blasts echoed through Tokyo-3, and the Angel collapsed on to the ground. Shinji stared at it, not moving. Suddenly it started shaking, rising from the ground, growing in size. It towered over the EVA, letting out a huge roar that deafened Shinji’s ears.
"What’s going on?? What do I do now??" Shinji screamed.
"Shinji, step back from it! Get away!" Misato’s face popped up through the viewscreen again.
"No! I can’t! I won’t run away, not now!" Shinji yelled back. He raised his EVA at full height, clutching the rifle. Suddenly there was a thundering crack and a brilliant light that hurt Shinji’s eyes. Shinji stepped back.

Shinji covered his eyes as the light whooshed toward him at a rapid pace. Soon all he could hear was a loud roar that hurt his ears. The light whipped behind him. After that there was just a silence and blackness all around him.
Shinji pulled his hands away from his eyes. "Whe…Where am I?"
He peered ahead. There was a silhouette of a woman – he couldn’t recognise who it was.
Then the figure started to blur and become unfocused and soon the blackness was replaced by the blinding light of the sun.
"Shinji!"
…Who?
Shinji was staring through the opened hatch of the Entry Plug. Misato’s face appeared.
"Shinji, are you all right?" she said.
"Yes…I just…" Shinji tried to get up, but couldn’t. His joints ached and his arms and legs felt heavy, like something was pushing them down. "…need to sleep…" Shinji closed his eyes.
Asuka peered over Misato’s shoulder. "Is he okay?"
"I don’t know. He’ll have to be examined." Misato said, standing back to let the paramedics move Shinji onto a stretcher.
"What actually happened? There was just a roar and a light, and my EVA wouldn’t move. It didn’t even budge." Asuka said.
"The EVAs will need to be examined and repaired. Especially Unit 01." Misato said. "It seems like the Angel’s blast did more damage than it should have, compared to other Angels."

"So how do the EVAs look?" Misato asked, walking up to where Ritsuko sat on the floor at the foot of Unit 01, typing at a board. Beside her was a clipboard full of notes and a cup of cold coffee.
Ritsuko looked up. "EVA Unit 02 and 00 are okay, there’s been no damage, but Unit 01…"
"What is it?" Misato knelt beside Ritsuko.
"There’s actually been more damage internally than externally, especially around the Entry Plug. It seems that the Angel was targeting either that or Shinji."
"Why would it want to get Shinji?"
"I don’t know. The Angel’s blast burned out the EVA’s wires in the butterfly handles and the hatch. The viewscreen needs some repair as well."
There was a silence.
"And there’s nothing left of the Angel?"
"Nope. It self destructed, leaving nothing behind except ashes." Ritsuko replied and continued working. Misato stood up, tilting her head up to look at the EVA.
"Look at it. It looks almost menacing." Misato commented.
Ritsuko kept working.
"I can’t help but feel there’s something more to the Evangelions than said. Much more." Misato said.
****
Shinji opened his eyes to find himself lying on an uncomfortable hospital bed surrounded in dull blue light. Cold sunlight filtered through the window. Shinji sat up. There was an odd feeling of uncertainty inside him, like a change he was not aware of. Shinji looked around him. What am I doing here?
There was a whoosh as the door opened and Misato stepped in, a tray in her hands. "Here, Shinji. It’s food." She set the tray on the table beside Shinji’s bed. "How are you feeling?"
"I don’t know…" Shinji scratched the back of his head.
"Well, Unit 01 needs some repairs. Especially the wires in the Entry Plug."
Shinji stared at her. What is she talking about? What happened?
"What’s the matter?" Misato asked. "What’s wrong?"
"I…" Suddenly Shinji found it hard to make his words. "…I don’t remember anything."
"Nothing at all?"
"Did…Did an Angel attack?"
Misato paused. She was getting worried. "Yes, it was an Angel. A powerful one, and you were caught in its blast. That’s why the EVA’s damaged."
Shinji was silent.
"Get some rest. You’ll be filled in on all the details of what happens when they come through." Misato said, standing up. She stared at Shinji. He looked different some how, empty. Misato knew it sounded ridiculous, but there was something missing. "You won’t be expected to be at school tomorrow. I have to go and get some work done."
She’s awfully sober, Shinji thought as Misato turned her heel and walked out of the room.
****
The door of Misato Katsuragi’s apartment slid open, where Touji and Kensuke stood waiting on the outside. They both took a step back when they saw who had answered.
"What’s your problem??" Asuka stood with her hands on her hips. A book bag was slung over her shoulder.
"Isn’t it obvious?" Touji said, crossing his arms.
"Where…Where’s Shinji??" Kensuke stuttered.
"Hey, what are you all doing here?"
Touji and Kensuke turned around to see who it was.
"Oh, it’s just the Class Rep." Touji said. Hikari stood behind them.
"Shinji isn’t going to school today, after what happened. He needs some rest." Asuka said, shoving between the two boys to greet her friend.
Touji and Kensuke glanced at each other and followed the two girls as the door to Misato’s apartment slid closed.
****
Shinji opened his eyes to be back in his familiar room in Misato’s apartment. He sat up from the futon, scratching the back of his head. It was awfully itchy, like something was lodged just under the skin. Then his fingers felt something unfamiliar. It was tiny, the size of his small fingernail, hard and square.
"What is this??" Shinji’s voice grew in alarm as he tried to dislodge it. But the small object was embedded deeply into his scalp.
His heart started beating wildly. There was something he didn’t like, he didn’t know what it was. Someone had done something to him that he was not aware of.
"Misato!!!" He screamed. "Misato!!!"
The door slid open, slamming against the wall. "Shinji! What’s the matter??" Misato’s voice came out alarmed as she rushed inside Shinji’s room.
"What is this? What did they do to me??" Shinji yelled.
"They didn’t do anything to you, Shinji, stop yelling!" Misato yelled back.
"What is this at the back of my head? What is it? Get it out!"
Misato was silent, her brows creased with worry. She stared at Shinji. Had he gone mad?
"Get it out!"
"Shinji…"
"I said get it out!" Shinji screamed.
"Shinji, there’s nothing in the back of your head."
Shinji reached back again to feel the back of his head. There was nothing. The itching pain was gone. "…What?"
"What’s gotten into you, Shinji?" Misato kneeled down beside the futon.
Shinji was silent. I don’t know…what’s wrong with me?

The whir of the air conditioners echoed through the Operations Room with the sounds of Ritsuko tapping on the keyboard.
"I don’t know what’s wrong with Shinji. He’s changed ever since the blast." Misato said, sitting on the table behind where Ritsuko sat. "He woke up screaming like mad this morning. He kept asking what they had done to him."
Ritsuko stopped typing. She turned around to stare at Misato. "Why did he ask that?"
"I don’t know. He kept screaming ‘get it out!’. I didn’t know what he was talking about." Misato replied.
"Strange," Ritsuko said, turning around and resuming her work.
Misato paused, staring at the back of Ritsuko’s head. "…So, how are the repairs on Unit 01 going?"
"Fine. Unit 01 will be finished by tomorrow afternoon. Let’s just hope no other angels attack until then or else it’ll just be up to Rei and Asuka to destroy it." Ritsuko said.
"And they can’t defeat an Angel without Shinji?" Misato said, getting off the table and walking toward the viewing window. In the opposite room, the three Evangelions stood bolted to the wall. There were ladders and ramps over Unit 01, but no workmen.
Ritsuko stopped typing. "That’s not what I meant, Major Katsuragi."
"I know what you meant."
There was another long silence.
Misato turned and headed for the door. "I’m leaving." The door slid open and she stepped out.

Chapter Two

"Hey, Shinji, you eating?" Misato yelled from the kitchen where a pot of water was boiling on the stove. Three bowls of instant ramen were sitting on the bench.
"I’m not hungry," Shinji said, emerging from the bathroom.
"Aw, now I’ve already prepared a bowl for you!" Misato said jokingly. Shinji continued walking to the living room where Asuka sat watching television. Misato frowned. Now something really is wrong, she thought.
Asuka lay on the couch, the remote control in her hand. She was flipping on the up-scroll button. "Don’t understand it…don’t understand it…don’t understand it…"
Asuka turned her head to see Shinji sit himself on the bamboo mat beside the couch. Bathed in the artificial light of the globe hanging from the ceiling, Shinji looked as tired as ever. Asuka could see the dark circles under his eyes, the drooping of his eyelids. Even his hair wasn’t the shiny blackish-brown it was before.
"You’re aging before your time, Shinji." Asuka said. "You tired?"
Shinji just threw a glance at Asuka’s direction then turned his head back to the television. "Are you okay?" Asuka said.
"Hm?" Shinji turned his head to look at her. "What do you mean?"
"I mean, are you okay? You look tired."
"I’m okay." Shinji said. The room became silent except for the blare of the television. Asuka’s eyebrow furrowed as she stared at Shinji. Something was up with him, she wasn’t even bothered with her usual obnoxious teasing. Asuka shook her head and turned back to the television.
****
TEST ACTIVATION OF ALL UNITS, THE NEXT AFTERNOON
Shinji grasped the butterfly handles of Eva Unit 01 as the Entry Plug filled with LCL. He breathed it in, feeling light-headed as the liquid filled his lungs. Shinji closed his eyes. Suddenly an image flashed before him. "What??"
No! I can’t run away, not now!
"Am I hearing things?" Probably. I’ve been so out of it lately. Suddenly Shinji’s eyes widened. Everything had turned black. "…What’s happening??"

"How is Shinji going?" Misato asked, standing a few metres away from the computer consoles.
"He’s okay. Harmonics are lower than usual, as well as the Synchronization rate." Maya replied.
"And Asuka?"
"Everything’s normal in Unit 02."
"What about Rei?"
"She’s doing well, too. It’s just Shinji who seems to be having trouble." Maya said.

Shinji looked around him again. Was he seeing things? Nothing was black, it was just the same old Entry Plug and the familiar smell of blood. And that strange humming sound.
Shinji shook his head. He felt so muddled up, so confused. What if an Angel were to attack, what would he do then?
"Shinji, is everything all right? Your synchronization rate has dropped." Misato said. Shinji looked at Misato’s image.
"I’m fine." He replied. "It’s just, I…" Shinji started to notice that the LCL had become discolored, tainted with orange. Shinji watched as the color grew darker to red. "What is this?!"
"What’s wrong?" Misato said.
"This…blood!" Shinji exclaimed. Clouds of red liquid danced through the LCL, filling his lungs. Shinji felt his stomach lurch. "It’s everywhere!"
"There’s nothing there, Shinji!" Misato said through the phone. She watched the screen, seeing Shinji look around him, his eyes wide.
"It’s blood! Get it out!" Shinji screamed.
Misato looked at the LCL filter screen. It said it was all clear. There was nothing there. "I said there’s nothing there."

The side of Shinji’s head began to throb with a sharp pain. Shinji screamed, squeezing his eyes shut. He tried to suppress it by putting pressure with his hand, but it was no use. The pain grew bigger, Shinji felt like his whole head was about to explode. "…My head!"

Suddenly all the lights flashed red and the sound of ringing filled the air.
"Emergency?!"
"Unit 01 – there’s something wrong!" Maya yelled. Suddenly the EVA’s eyes lit up. Tilting its head, it let out a huge roar.
"Quick! Eject the Entry Plug." Misato ordered. She clutched the phone handle, watching as the Unit 01 released itself from the holds.
"It’s not responding – it’s gone berserk!"
Unit 01 stood in the centre of the room, clutching its head. A noise was coming from it, like a scream of pain.
"Powering down in five seconds." Hyouga said. "Four…
"…Three…two…"
With a loud crack, the EVA rammed its head into the ground, breaking the cement. Black lines splintered through the white cement.
"…One…"
Everything was silent, flashes of red lighting up the room.
"…Shinji?" Asuka’s shaky voice came through the speaker and echoing through the room.
"Is he all right?" Rei’s quiet voice asked.
"I’m not sure. Everything’s gone dead." Misato said. She leaned against the glass, peering at the Angel. Something wasn’t right.
Unit 01’s hand started moving.
"No…!"
Movement broke out throughout its whole body and the EVA stood up, letting out an earsplitting roar that sounded part human and part beast. Fragments of cement fell to the ground, the EVA’s eyes lighting up with a sharp noise.
"But that’s….That’s impossible!" Maya exclaimed.
 The door whooshed open and Ritsuko stepped in. "What’s going on?"
"Unit 01 – it’s gone crazy!"
"Misato!!!" Asuka called. "Look!"
Blue light seemed to appear out of nowhere, wrapping around EVA Unit 01. They stared as Unit 01 tranformed before them, it's eyes growing in yellow brightness as it let out another roar.
Asuka stared at it. It looked different somehow, she knew it sounded silly, but more...evil. Far more than the time when he burst out of that last angel, blood dripping from its body to the ground.
Tentacles burst out of Unit 01's torso, and from its back spurted red-glowing wings. There was a flash of light and what used to be Unit 01 now stood a creature that looked part serpent part dragon and gleaming red.

"What the hell??" Misato yelled. The computers blinked on and Ritsuko quickly tapped in a few keys.
"It’s being confirmed now. Blood type: blue." Ritsuko said. She looked at Misato. "What do you suppose we do now, Major?"
"That’s impossible…impossible…it’s right here, an Angel!" Maya said.
"It happened before, it’s happening again,"
"Misato!!! Misato!!! Get us out of here!" Asuka screamed through the speaker.
"We’ve got to get those kids out of there."
"No. If we do, how will we defeat this thing?" Ritsuko said. There was a silence and the noise of the emergency beeps grew louder.
"Start full activation of Units 00 and 02." Misato ordered.
"Yes, ma’am."
"How do we get Unit 01 and the pilot out of there?"

Chapter Three

The throbbing pain wasn’t in his head anymore, it was around his whole body. Shinji gritted his teeth, closing his eyes. He noticed there was that itching pain at the back of his head again. Just concentrate…don’t think about it.
"But I can’t. It’s too much!" Shinji screamed. He opened his eyes, his pupils dilating. He wasn’t in the Entry Plug anymore. He was floating in midair, a soft light surrounding him. The pain was gone. He was swimming in a warm, thick liquid. Where am I?

The Angel had disappeared. In a flash of yellow light, it had gone.
"It can't have!" Ritsuko said. "It's not..."
"An unidentified object has been sighted on the outskirts of Tokyo 3." Hyouga said.
"You mean it...?" Misato said.
"Just perfect." Ritsuko said, a gleam in her eye.
"Why would it go outside of NERV when it was just where it wanted?" Misato asked herself.

Tokyo 3 had gone completely silent; everyone was hiding out in their emergency shelters.
Beeping noises filled the air and the doors of a makeshift building slowly slid open, revealing the two EVAs.
"Just keep heading to the west." Ritsuko said through the speakers. "You're sure to spot it in a couple of seconds."
Asuka's eyes widened. "Too late."
The two EVAs quickly dodged the buildings agilely, missing the tentacles of electricity the Angel whipped out every now and again.
"Rei – watch out!" Asuka screamed.
The blue and white EVA quickly jumped over a building like it was a hurdle, a tentacle whipping around, narrowly missing the EVA.
"I’m okay." Rei said, breathing hard.
"Internal battery’s running out." Asuka said. "Switching to external power."
"Dammit, where is it?" Asuka murmured to herself. She scanned the buildings, and there it was – the power cable. Asuka grabbed hold of it and inserted the cable into the back of her Evangelion. Rei did the same.

"I’m giving you both rifles. Be ready." Misato said. She flicked a button and outside, two doors slid open on a building, revealing the impossibly large rifles.
Asuka grabbed one of them and threw the other to Rei swiftly. Asuka aimed. There was a click and she pressed the trigger.

"Results are coming in right now."
The whole team of the operations unit sat together as the computer printed out sheet after sheet of paper.
"This Angel has the ability to remove its ‘soul’ from its physical body." Ritsuko said. "Since the EVAs are controlled by the minds of the pilots, the Angel’s soul has found a place to stay. This, of course, was its intention: to get into an EVA and destroy NERV from there."
"Then why did it get out of NERV and outside?"
"I'm not sure. But, it must have plans."
"Clever." Misato commented. "What happens to the EVA?"
"The EVA has become apart of the Angel now. So if we destroy the Angel, we must destroy the EVA."
"But the pilot – Shinji! You can’t do that." Misato protested.
"How do you propose we get Shinji out then?" Ritsuko asked.
"Anything but that. I am head of the Operations Unit. Destroying the Angel is out of the question!" Misato yelled.
"This Angel could destroy the whole of Tokyo 3. Are we going to risk that just to let one person live?!"
Everyone was silent.
"I’ll consult Commander Ikari. See what comes up from there." Misato said.

"Do whatever you think is necessary to destroy that Angel. Do not worry about the pilot." Commander Ikari said behind his desk. Underneath the glass floor they were standing on was the Geo Front.
"But Sir, Shinji could die." Misato said.
"And so could the population of Tokyo 3. This could turn out into the Third Impact." Ikari said. "Do everything you can to stop that Angel. And don’t worry about the pilot. He’ll survive."

Shinji breathed in the musty smell. What was it? It was like LCL, but thicker, and warmer. It had a peach color to it. And that sound, what was it? Where was he?
It was so much like the Entry Plug, but different. There was no smell of blood. He felt comfortable. Shinji closed his eyes. I’m so tired.
There was a flash. An image appeared before his eyes, a silhouette of a small boy. "You're..."
Shinji opened his eyes. Was that his mind...or something else? "...not..."
"I'm not what?!"
                                                                                      "...Shinji."
"I'm Shinji! I'm Shinji Ikari!" Shinji screamed.
"YOU'RE NOT SHINJI IKARI!!!"
Suddenly there was a cracking pain at the side of his head. Shinji screamed, holding his head between his hands, squeezing his eyes shut. "STOP IT! STOP IT!"
The pain stopped. Everything became silent when Shinji opened his eyes.
"You will never be Shinji Ikari...
                                                                        ...again."

The bullets bounced off the invisible shield created by the Angel. Orange circles rippled around where the bullets had tried to penetrate.
"Expand your AT Field!" Asuka said to Rei.
"Got it."
There were crushing sounds as everything in a couple of metres radius of the EVAs were destroyed.
Asuka looked up at the viewscreen. Her eyes widened. Where the Angel had been, EVA Unit 01 stood. "Misato, what do we do now?!"
"Maybe it’s an illusion." Rei said.
"Maybe?!" Asuka screamed.

"Rei’s right. The image of EVA Unit 01 is just an illusion. It’s apart of the Angel’s AT Field, designed to trick others so they won’t be able to penetrate it." Ritsuko said. She glanced at the computer screen again.
"We’ve got contact with Unit 01!" Maya called out to Misato.
Misato grabbed the phone. "Shinji! Shinji, can you hear me?!"

Shinji's breaths quickened. "I will never be...Shinji Ikari? But I am Shinji Ikari. I have always been Shinji Ikari...right?"
Shinji looked around him. Had he gone crazy? He was talking to nobody but himself.
There was a crackle and he could hear Misato’s voice through the speakers.
"M…Misato?" He barely whispered.

"Please reply, Shinji. Are you all right?" Misato said. There was still static. Misato put the phone down. "No answer!"

I’m gonna die soon…I don’t know how I know, there’s just a feeling in the back of my mouth…
Shinji could hear the crackle of static stop. No…no!
"Misato!" Shinji screamed. "Misato, are you still there?!"
No, no…there’s still hope…right? "Get me out of here, Misato!!"
The itching pain at the back of Shinji’s neck grew. "Aaaaaagh!" He clawed at the back of his head. "What is this?! Get it out!"
Shinji looked at his hands. Blood…and something else. Shinji looked closely at it. It was small, as big as his little fingernail, square and metallic. There was writing on it. Property of NERV. "What?!"

Chapter Four

The image of Unit 01 had vanished. Asuka breathed hard, staring at the Angel, its flowing tentacles, its glowing wings. It was unlike any other Angel she had seen before, and far better than any other Angel in battle. Asuka’s brain felt weary, but she was determined to defeat it.
Taking a step forward, she reached for her progressive knife. Extending it, she stood in front of the Angel, prepared. “Rei, when I say go, shoot at it.”
“You’re not going to..”
“…I’m going to try to break it’s AT Field. When I say it, shoot.” Asuka said. She took a deep breath and ran toward the Angel, the cement crunching under Unit 02’s feet. Taking a leap in the air, she surged the knife down on the Angel. “Aaaaaaaarrrgghhhh!!!!!!”
The invisible wall of the AT Field glowed a orange-yellow as the knife sliced through it, disintegrating it into nothing. “Rei – do it now!” Asuka quickly dodged out of the way.
Unit 00 stood with its feet apart, clutching the rifle. Rei pressed the trigger and the blasts echoed through the empty Tokyo-3.

Shinji stared at the object in his hands. Blood was all over them. "…What?! What…is this??”
The speakers crackled in the Operations Unit room. Misato looked up. She could hear Shinji’s faint voice through the static, sounding like something between a gasp and a sob. “What is this?? What did they do to me?!”
Ritsuko froze. He’s found it!

Bullets struck the Angel’s upper body. The Angel screamed – more like roared, falling from the sky and landing heavily onto the cement. The round ball of core glowed an orange-reddish color, and quickly brightened to bright yellow. Rei squeezed her eyes shut, the blast echoing through her ears.

“The Angel self destructed!” Maya yelled out from her seat.
“No!” Ritsuko screamed. “It can’t! It…”
“Shinji!” Misato yelled.

When the light faded, Asuka uncovered her eyes. Her eyes widened. Standing in the middle of the debris was Unit 01. Is it…a fake? Or is it real?
The three EVAs stood there, unsure of what to do.

“That’s the real Unit 01.” Ritsuko said.
“Everything is normal, ma’am.” Maya said.
“And Shinji?” Misato asked.
“Readings should be coming in in a few seconds.” Shigeru said.
Misato waited…and waited. “Well? Why is it taking so long?”
“I don’t know. It’s…it’s not responding.”
Misato gave a sigh of annoyance. “Damnit!”

Shinji stared at the two EVAs in the viewscreen. They weren’t Unit 00 or Unit 02. They were exact replicas of Unit 01. “What the…?! If they are there then…who am I?!”
    …who am I?
      …WHO AM I??
“Who am I?!? I am Shinji Ikari!” Shinji screamed. “I am…I am an imposter…?”
He glanced up again at the two EVAs. His eyes widened as the two melded together to form one complete EVA.
You are not Shinji.
I am Shinji.
You will never be Shinji Ikari.
“I AM SHINJI IKARI!!!!!!” Shinji’s EVA began to rear up, running towards the fake Unit 01. Shinji grasped the butterfly handles, staining them with blood. The small metal object fell to the floor of the cockpit.
Shinji grabbed the left arm of the other EVA, squeezing it, hearing the screech of the metal as he snapped it. Pain shot through Shinji’s left arm. “Aaaaargh!!!!”

Asuka squinted her eyes. Has it gone crazy…again? What is Shinji doing??

Which arm? Which was his?
Shinji looked up. The imposter EVA had vanished. “It’s…it’s gone…but I am still here.” He did not realize he was still clutching his left arm, which had gone numb. With a final crash, EVA Unit 01 fell head first onto the ground, it’s arms laying limp at its side and its rear in the air. The glow in its eyes faded as Unit 01 de-activated itself.
“I am still alive.” Shinji breathed before he fell unconscious.

Tears ran down Misato’s cheeks, staining her black dress with dark spots. “Oh my god, Shinji! Are you okay?”
A feeling of déjà vu swept over Misato. This is just like before…
The sun was fading into the horizon, painting the sky with brilliant shades of orange and purple. Misato stood back and watched as Shinji was carried onto a stretcher. She noticed the blood on Shinji’s hands. “What went on in there?” Misato asked herself. What was he talking about?
She could hear Shinji’s words in her ears. What was that? There’s so many things I don’t know!

**************************
To be continued...

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