Hello everyone and welcome to Evangelion: (Never) Alone Part 2!

Before we begin I want to quickly apologise for the formatting of this chapter. I had to finish this on my phone on the way to work to get it out on time and I never really liked the formatting FF's mobile app. I promise to get it fixed when I return home

If you're new to my work and have decided to start off with this story then I recommend reading the one that came before it: (Never) Alone. It's not vital, as this first chapter will fill you in on the events of (Never) Alone, but it should help you understand what's going on here.

Evangelion

Gemini Rising

By Rollinaround

Episode 1

Tales From Another BrokenHome

"Alright," said Ritsuko, "I'm just going to ask you a few simple questions to confirm your identity." Across from her sat a thin boy in his early teens, beside her; a one-eyed redhead in a skintight plugsuit. "Now, to start off, please state your age and date of birth."

"June 6th, 2001." Shinji said, as Second Lieutenant Suzuhara inspected his wounds, "I'm 14 years old."

"Correct. Now, can you tell me who brought you up?"

"I lived with Yui and Gendo Ikari for the first couple years of my life," he began, "My Mother was absorbed into Unit when I was 3, and my Dad... my Dad abandoned me about a year later." He stared at the floor. It was over a decade ago (from his perspective), but still a painful memory. "After that I moved to Kyoto to live with my Aunt and Uncle. But I wouldn't say they raised me; we almost never talked, or even saw each other."

Ritsuko marked down each of his answers, stoicly, robotically. "Any people close to you? Anyone you might consider a friend, or family?"

"My friends are Kensuke Aida and..." He felt Sakura tighten her grip on him. She'd maintained her bedside manner since he came back onboard, but her warm and friendly demeanor had gone. "I was friends with Touji Suzuhara back in 2015. Misato Katsuragi looked after me during my time as an Eva Pilot, and I had a crush on Rei Ayanami, the real one." He looked over at his former co-pilot. It was hard to tell what Asuka was feeling at any given moment, because she always looked angry. "I was also friends with Asuka Shikinami at the time."

"Alright, one more test." the Doctor said, "Tell me something only we know. Ideally, this should be something from before Third Impact."

Shinji struggled with this one. He hadn't spent much time with Ritsuko, so she couldn't confirm anything he told her, and he'd known Sakura for less than a day. Asuka was his best bet, and only one particular memory stood out in his mind. "The night of the 8th Angel attack, Asuka Shikinami um, slept in the same bedroom as me..." Asuka's face burned red with embarrassment, or rage (he couldn't tell which) "Uh, platonically I mean!"

The Second Child took a deep breath. "You're lucky you caught that, Bratty Shinji." she grumbled. "What he says is true. It's him."

"Thank you Shinji." Ritsuko said, tucking her notebook into her jacket, "That will be all for now. How is he looking Suzuhara?"

"A bit malnourished, but other than that he's mostly unharmed." Sakura replied. "Honestly, it's a miracle he got out alive. There's evidence of lacerations on his right forearm, but they're in really odd positions; they don't look like they were the result of an attack, nor could they be self inflicted."

"Oh those," Shinji said, "I got those a few weeks ago. I, punched through a sheet of metal."

Sakura gave him a very blank stare. "Why?"

"It was training." he explained. "My Sensei wanted to see how hard I could punch."

"How... why- forget it." The Medical Officer threw up her hands. "I don't even want to know." She bowed, and left the room without another word.

"You will explain your actions to the Captain later this evening." Ritsuko said, "Every available man and woman will be there, and the hearing will be broadcast across the world tomorrow morning. The guards will arrive to collect you at 1900 hours tonight. Do you understand?"

"Y- yes Ma'am..." The boy shuddered at the thought of it. Was he being put on trial? Asuka told him Misato was on his side, but a Not Guilty verdict seemed impossible and he dreaded to think what sentence would fit the crime of Omnicide.

"You can relax." Ritsuko said, "WILLE doesn't have the authority to sentence you. Only the United Nations can do that."

"That's not very encouraging."

"You aren't going to be executed Shinji." Ritsuko promised, "The UN isn't about to kill a child, regardless of his actions."

"Thanks." he murmured, "That makes it, a little better."

"The real purpose of this is to let the world hear your side of the story." she explained, "Mankind's feeling towards you are, mixed at best. Depending on what you tell us, you might convince them you're worth another chance."

Shinji doubted it. After everything that happened in the past few months, even he wondered if he deserved another chance.

"Alright, let's take it from the top," Misato said, looking through the report Asuka had given her. "Captain Shikinami tells me that at roughly 0900 hours on the date of April 17th 2029, you removed the Spears of Longinus from the Lilith against the protests of both Shikinami, and your co-pilot. Is this correct?"

Shinji stood a couple floors below her, seemingly tiny as the men and women of WILLE looked down on him. "It is." he admitted.

"Can you explain why you decided to take the Spears?"

"Yes Mi- Colonel." the boy replied, staring up at the crew above him. They just stared back, regarding him cautiously. "The other Pilot, Kaworu Nagisa, told me that if we had the Spears, we could use Eva 13 to reset the world back to how it was before."

"And you took the word of this boy at face value? Why?" The Colonel couldn't imagine a logical reason.

"Because he was nice to me." Shinji told her.

Misato was incredulous. "Is that it? You couldn't have known him for more than a few days."

"I was lonely, alright?" the boy moaned, "All my other friends were either dead or hated me."

"So why didn't you listen when he told you to stop?"

Shinji looked uncomfortable, like he was struggling to accept the truth. "I was desperate. I wanted make up for what I did, I... I wanted to be forgiven."

Captain Katsuragi rubbed her temple. The things that boy would do for affection. "Let's move on: can you tell us exactly how you survived your suicide attempt the following day."

He shrugged. "I'm not really sure. I just remember seeing a flash of orange light, just before I hit the water. If I had to guess, I think I subconsciously manifested an A.T Field."

"We heard about that." said Misato, "Captain Shikinami claims you gained your powers from the 10th Angel?"

"Zeruel, yes. He said he followed me out of Unit 01. He started talking to me just after Fourth Impact (though I hadn't realized it); said the DSS Choker had been keeping him suppressed."

"That reminds me." Ritsuko chimed in, "What happened to the Choker? Only Captain Katsuragi should have been able to remove it." The boy looked, mournful.

"Kaworu (my co-pilot), he took it off me..."

"That's impossible," Ritsuko insisted, "Nobody without the proper authorization should be able to remove the choker without-" Misato cut her off. Shinji was crying. "I suppose it doesn't matter how. Do you feel you can continue?"

He agreed to carry on, though he didn't look very enthused.

"There's a large gap in the story between your fall and the time when Shikinami found you." the Captain said, "Can you tell us what you were doing during that time?"

"I woke up in the slums of Elysium a little while later. Some people took me in and nursed me back to full health. They knew who I was, but they didn't care. They knew what I'd done, but they didn't hate me for it." The boy stayed calm, but there was more than a hint of bitterness mixed in. "I ended up working on the farm for a little while until, I got involved with Itachi..."

"And?"

He did his best to keep it short. "I went out one night to find his men beating on the other farmers. I tried to stop them, and got myself knocked out. After that, Zeruel spoke to me in a dream, and offered me his power in exchange for letting him into my conscious mind." The crew exchanged nervous looks, and Misato couldn't blame them.

"And you accepted?" she asked him, "Do you realize what you could have done?"

"Of course I do." Shinji replied, "But I was tired of seeing my friends get hurt and not being able to stop it."

The Colonel gritted her teeth. Thinking ahead was never Shinji's strong point but somehow he found a way to keep pushing the envelope again and again when it came to bad decisions. "Alright..." she said, after she counted to twenty, "Then what happened?"

"After that," the child said, "I got into another fight with Itachi's men, after they threatened to kill the the Mayor came down to the slums asked me to work for him. He said he'd hurt my friends if I refused."

"And what did you tell him?"

Shinji didn't even bother to hide the satisfaction on his face. "I threw him across the room, said I'd kill him if he threatened the village again." Misato repressed a smile. After being made to kowtow to Itachi for the better part of a decade, she liked the idea of him getting his ass beat.

"In the middle of all this, I started training with a farmer called Wilson Clarke. He taight me to be a better fighter. A while later, the Mayor cut off the water to the slums until they turned me in. Instead, I went into the main city and crashed the Water Treatment Plant. I almost made it out, until I got tranqued." He stared meaningfully at his old school friend, Kensuke Aida. Kensuke had been working undercover in Elysium, searching for a link between Itachi and NERV, and had been partly responsible for the boy's capture.

"I was kept in prison for I don't know how long." he continued, "Every day they made me fight one of the villagers, until I... I had to fight Mr Clarke and..."

He was beginning to tear up again. "It's alright Shinji." Misato assured him, "I think I understand. Let's finish this up, what happened after the Captain found you?"

Shinji wiped away the tears, but his body was still trembling. "After that, A- Asuka got thrown in prison with me. They made us fight each other the next day but we broke out. I..." He swallowed. He wasn't just sad, now he was frightened. "My body went into a Pseudo Awakened state." The room fell deathly silent.

"Around this time," Ritsuko told him, "The Wunder did battle with a new Evangelion prototype from NERV. We were about to lose until Eva 01 Awakened. I assume you had something to do with this?"

"Probably." the former Pilot said, unable to even look at Katsuragi: the woman who was practically a Mother to him. "Zeruel told me that I could Awaken Unit 01 if I didn't control myself. And towards the end, I just lost it."

The crew were horrified and Misato could not blame them. On the one hand, he'd single handedly saved them from certain death. On the other, he had made himself more dangerous than ever. "Shinji..." she groaned, burying her face in her hand.

Ritsuko, however, remained calm. "And what did you do to Itachi?"

"I chased him down." Shinji recounted, "He tried to leave the city in a helicopter but I cut him off. I beat him almost to death..." He started to breathe heavily, and clenched his fist so hard he almost drew blood. "He begged me to stop but that just... just pissed me off even more! I grabbed the guy and almost fed him into the helicopter blades. I wanted so badly to kill him..."

The Colonel's eyes went wide. She'd never heard him talk that way before. "What stopped you?"

"I, thought of all the friends I lost, everyone who'd died because of my mistakes, and I couldn't do it. I felt like I didn't deserve to take another life." Misato adjusted her hat, hiding her face. She couldn't afford to be seen as soft.

"Is that everything?" she asked him.

"Yes."

Misato was at a loss. What were they going to do with him? "Do you have anything else to say?"

The teen stepped closer. "I know I messed up." he said, "I know I have to take at least some of the blame for Third Impact, and I can't deny the Fourth Impact was my fault. And I am so, so sorry for the people I've hurt. But I'm not a monster! I'm just some stupid kid who lost everyone he loved because he tried to do the right thing. And I shouldn't be scapegoated for something I never even wanted." Shinji choked back his tears. There was sorrow in his voice, and anger, and bitterness, and even guilt and remorse.

"I'm not trying to shift the blame or avoid responsibility..." He said, "I know that I've done terrible things, even if I didn't mean to. I know you're the worlds best hope for stopping my father, and the world is safer if I'm in your custody." He stared up at the woman who, in just a short span of time, had become perhaps the most important person in his life. "And I know there are good people on this ship, people I still care about in spite of how they treated me."

The Captain looked away in shame. Of all the things he could have said, that hurt Misato Katsuragi the most. Being hated for what sge did would be painful. But knowing that he still cared, despite what she did, that was a dagger in her heart.

"That's why I came back." Shinji said, finally, "I want to make things right, I want to help in any way I can. Please, let me help."

Misato looked away in shame. Her crew were silent as the grave. "We will see..." she said, before she let the mask slip. "You may leave now Shinji, we will determine what to do about you soon. Suzuhara?"

The Second Lieutenant bowed, and lead the boy out. Officially, he was under house arrest, held in a room just below the barracks. Fairly mediocre accommodations but better than a cell, and his location would be known only to people she trusted, giving Shinji some much needed safety and privacy. With the hearing ended, she sent her crew back to their posts, while she and Ritsuko returned to the Captain's quarters.

"That could have gone a lot better..." said Misato, nursing a growing headache.

"It could have gone a lot worse." Ritsuko said.

"How do you figure?" the Captain asked, "He openly admitted to letting an Angel into his mind, and remotely awakening Unit 01."

"He also admitted his fault in causing Third Impact, and expressed a desire to help us."

"And how is he supposed to do that now?" Misato shot back. "Any role he might play would need him to interact with the rest of the crew. How do you expect to keep him safe?"

A cunning smile appeared on the Doctor's face as she adjusted her glasses. "Don't worry about that, I've got a few ideas."

Gendo Ikari sat in the lower levels of NERV HQ, staring up at the giant tube of LCL. In it floated a pale, half-formed humanoid, slowly increasing in size with every passing day. The Project was just the latest in a long line of Artificial Humans, but this one was special.

"Is it ready?" he asked, turning to the Vice Commander.

"Not quite." said Fuyutsuki, "We still need to wait a few more days until we begin work on the final stage of development. We've never attempted to program one of our experiments with a specific personality before, so we don't know what to expect."

"We can afford to wait." the Commander said, "What of the Mass Produced Evangelions?"

"Almost finished." Fuyutsuki replied, "Just ironing out the last few errors left over from the prototype, then they'll be ready for deployment."

"Excellent." Ikari said, leaning back in his chair, watching intently as Project Gemini stirred in it's tube.

It's good to be back again. I hope you all enjoyed this first chapter in the continuing saga of (Never) Alone.

One of the difficulties with writing a sequel fic to 3.0 is that a lot of the characters actions are left open to interpretation, and when your own interpretation differs fron your reader's, it can be very hard to balance your own vision with what the fans wanted to see.

In this case, a lot of people wanted to see Shinji hate Misato, or in one case, straight up attack her, and personally I couldn't see Shinji doing that. I had initially written Shinji as being more apologetic and blaming himself for everything went wrong but I quickly realized that would be really unsatisfying. In the end I compromised and went with the "killing with kindness" approach, having Shinji still care for Misato despite her poor treatment of him, resulting in her shaming herself.

That's all for now, I look forward to seeing you guys again soon in Chapter 2

-Rollinaround