The most authoritative argument about Mari's role is from the 2.0 CRC as in she is a "Miko-san [shrine maiden] channeling the gods". When you take into account of her previous encounters with Lilith, that argument makes it sound very much like Mari's is actually an agent of Lilith, willingly or unwittingly.

In 2.0 after she ejected from Unit-05, she said to herself "I'm a little hesitant/worried/sorry about involving an adult/adults in my affairs/for my motives." My interpretation is that she was willing to fight against Tunniel and almost get killed for her own motives. That also implies the motives would be something important as her mission for life and are somewhat different from Kaji's (but allied). However, these motives are never mentioned again later. I won't be surprised if her ulterior motives are something ultimate and grand beyond just protecting the Children, like assisting Lilith's scenario, which runs in parallels to SEELE's plan and Gendo's plan. Because Lilith is very much sentient in this fanfic, it is entirely plausible that Lilith is also an active plot-driving actor to have her own scenario (fight against Adams?).

So how does fighting against Tunniel help with her mission? This was a scenario designed by Gendo to 1) steal Nebuchadnezzar's Key and 2) destroy Unit-05 and it was executed by Kaji and assisted by Mari. It's possible she knew how Neb's Key worked and decided turning it to Gendo's hand would help with her cause, in the case that she is truly the envoy of Lilith with god's knowledge. Or it's also possible she didn't know but she wanted to do Gendo a favor in exchange for his tacit agreement that she could go to NERV HQ, in the case that she's unwittingly acting under Lilith's latent influence. Later NERV's staff and the Children didn't know her at all until Wille (Gendo should know everything as cunning as he always is). This is probably because Gendo wouldn't allow her getting anywhere near in the first place again probably because Gendo knew she was very dangerous by knowing so much or being associated with a spy, so she probably had to do the favor in order to do anything.

When I looked at the context around the above dialogue, several things stand out. Unit-05 is the "first time" when she piloted any Eva and her piloting skills are superb without prior experience. ("syncing with an Eva was really more intense than people say." She had synced with a core but she hadn't experienced the synced pain in combat.) The only plausible explanation I can think of is she acquired certain special abilities during the time when she stayed in the core of Unit-XP for her to be a natural to sync with any Eva. Another unexplained thing is her eagerness to pilot or how she piloted for fun. This seems not very consistent with her previous unpleasant stay with Lilith. Indeed, this part of her character can use some backstories to explain and show what kind of fun that is and where it comes from. Apparently this fun is different from being comfortable sitting in mom's lap as in the case for Shinji and Asuka.

There is also a weird situation for MariRei as Rei has Yui's body but Lilith's soul. I'm not exactly sure how Mari felt towards Lilith as it appears Mari would hate her because of all the mind rapes, but those mind rapes didn't look really painful to be honest (because I didn't see them have a lasting effect, Mari didn't have a total breakdown, didn't get incapacitated, didn't have nightmares, as Asuka did). Or maybe Rei only had the benign part of Lilith's soul while the sadistic part was some other part related to Unit-00/Rei I's soul.

Excerpt from Episode IV: The Last Hope – Chapter 5 – School of Hard Knocks; Shamshel Attacks

Misato and Shinji were on their way back home from NERV. They had just gotten off the car train, and were exiting the access tunnel.

“Shinji, how was school today?” Misato asked.

“It was ok.” Shinji replied while staring blankly out the window.

“Are you sure? You sound kinda down.” Misato gave him a worried glance. “Are you sure everything there is going ok? You can tell me anything, Shinji, I’m here to help you…”

“Its fine, I keep to myself mostly.” Shinji replied. “Its way better than my old school, they never left me alone there, always teasing me and hitting me, it’s nice to be… invisible.”

“You used to get hit?!” Misato shouted. “Why did nobody do anything?! What about your old guardian?! Why didn’t he step in?!”

“I never told him, he couldn’t do anything anyway. The teachers never did, they just saw me as the child of Gendo Ikari – Wife Murderer. I was judged because of him, and I couldn’t do anything about it.” Shinji kept staring out the window. “Besides, I can handle myself. It happened for long enough, it doesn’t even hurt anymore…”

‘Shinji…’ Misato thought. ‘Life hasn’t been fair to either, has it? I guess we really are a lot alike, almost like destiny brought two souls together to help one another…’

“Is the story getting too real for you, Misato?” Shinji asked. “Or is something wrong with you.”

Misato looked over at Shinji again. “What do you mean? I just…”

“Couldn’t think of a way to make me feel better?” Shinji asked. “It doesn’t matter, as long as people leave me alone, I’m just fine! Friends just end up disappearing and leaving you… alone…” Shinji said sullenly as a tear rolled down his eye. ‘Like that girl from so long ago…’ Shinji thought. ‘Why did she leave me?’

“Shinji… I’m sorry.” Misato replied. “I just…”

“Just pull over here, I have to pick stuff up for dinner.” Shinji said gruffly. “I’ll walk the rest of the way back.”
–––
Misato was taking a shower after dropping Shinji off on the side of the road. While she was soaping herself up, she was talking to herself about Shinji.

“I wonder what’s up with Shinji…” Misato said to the shower wall. “I mean, he’s sometimes so quiet, and sometimes he’s a dick, but he’s been through so much. His file mentions nothing, save for his mother’s death and father abandonment… I guess he just needs a friend, but I can’t be his friend… I just don’t get him… I want to help him so badly, but I’m just not sure how to. He’s not exactly open about things…”

Misato rinsed the soap off herself and sighed. “Well, at least a nice hot shower at the end of a long day can make things better… maybe I’ll just take a bath later too, to relax. I wish I knew what could calm Shinji down though…he’s so tightly wound, it’s only a matter of time before he snaps and does something… drastic.”

Shinji was walking towards the apartment. ‘I hope Misato’s not mad.’ Shinji thought. ‘But, she was asking questions she wasn’t prepared to hear the answer to. Sometimes the truth is just harsh, there’s no way around it.’ He pushed open the door and walked into the apartment. Shinji realized he didn’t actually unlock the door. ‘Great, she left the door unlocked again. Someone could just walk in, like any perv off the street. Misato is just so careless. Whatever…’

Shinji wake silently into the kitchen, after locking the front door. Shinji got hard to work on dinner, and beginning to cook a simple stir–fry. Pen–Pen waddled up to Shinji while he was cooking and began to pull at his pants leg.

“Wark!” Pen–Pen squawked sullenly.

“Oh, hello Pen–Pen.” Shinji replied to the sad bird “I bet you’re hungry, aren’t you?”

“Wark, wark!” Pen–Pen squawked in reply.

Shinji went into the fridge and gabbed a package of beef jerky. “I got this especially for you. I figured since the package disappeared, you might like one to yourself.”

Pen–Pen wrapped his fins around Shinji’s leg. “WARK!”

Shinji patted Pen–Pen’s head. “You’re welcome.” Shinji replied, as Pen–Pen ran off to the couch and ripped open the package of jerky, eating all of it in a rush before slumping over in a happy daze. “Silly bird…”

Shinji kept cooking while Misato got dressed. ‘So, he came back without saying hello. Guess he’s still mad…’ Misato thought as she went out into the kitchen to relax. She grabbed three beers from the fridge, and cracked one open and chugged it. “Ahhhhh!” Misato exclaimed. “There is nothing like a cold beer after a hot shower, right Shinji?”

“Misato, I don’t drink.” Shinji said as he served dinner. “I’m a minor, remember?”

“You’re no fun.” Misato replied, digging into her dinner. “So, Ritsuko called me with some results from today’s test. You’re reaction time has improved incredibly since you started piloting. But one area of improvement she can see is, you need to respond faster to orders. That lack of response time is dangerous, and could become a problem down the line.”

“I can’t help it, Misato.” Shinji replied. “I’m just not cut out for this shit. Besides, it’s not like I’m piloting because I want to.”

‘I thought he was piloting because he wanted to… I’ve got to set him straight…’ Misato thought as she stared at Shinji in shock. “What kind thinking is that, Shinji?!” Misato shouted. “The lives of all mankind are riding on you as a pilot, if you think like that in combat, you’re liable to get yourself killed!”

“Whatever, I don’t really care.” Shinji replied as he played with his food. “It doesn’t matter when I die, it’ll happen when it’s supposed to, EVA or not.”

Misato slammed her beer down and stood up. “What the hell kind of thinking is that?! You may be open and accepting of death, but the rest of us aren’t quite as accepting of that. You’re an important pilot to us, your life is no longer yours to live! I don’t want you to die, stop thinking that way!”

Shinji swiped his hand across the table, sweeping his plate off the table and leaving a mess on the floor of his uneaten food. His face looked livid as he stood up and silently walked away from Misato. ‘So I belong to them, do I?’ Shinji thought. ‘And here I thought Misato took me in because she liked me… does anyone in the world care about me?’

“Hey, I’m talking to you Shinji where the hell do you think you’re going?” Misato asked.

“Bed.” Shinji replied angrily. “I’m done with this conversation. You made your point very clear, nothing is my decision anymore, and can only die if I’m ordered to. Just go out and kill angels, and eventually, I’ll be told I can be in control of my life again, if I don’t die before hand. I’ll see you in the morning.”

“Shinji, get back here and clean up this mess!” Misato shouted.

“It’s your turn for cleanup tonight, Misato, look at that chart of yours.” Shinji said coldly. “Goodnight…” Shinji slammed the door to his room. ‘It’s not like I have anything worth fighting for anyway…’ He thought he laid back on his bed and looked at the ceiling.

Shinji left Misato standing alone and confused. “What did I just do?” Misato muttered. “I was just trying to motivate him…”

Shinji is definitely a bit more quick to anger than expected.

Careful here. Big difference with Shinji's characterization.

What I see here is a jaded, cynical, confrontational, destructive, full-blown sarcastic Shinji. NGE!Shinji is passive, approval seeking, good-hearted, clinging.

NGE!Shinji's personality is shaped by past abandonment, solitude, lack of social interaction or social anything. His story of growth is about coming out of his shell to face the reality and experience hurt in getting close to others. This Shinji's personality is shaped by past hostility, solitude, social isolation. What is his story of growth going to be?

Not saying this is not workable since we probably have a time loop theory going on for this Shinji to be a different incarnation and have different background, it's just things need to be looked after carefully to have a meaningful connection to the canon without making this character being perceived totally removed from the original one.

For any one whose a bit surprised by the authors Shinj being more aggressive and forward you may want to check out the Manga as he's much more angry and sassy in there and I believe that is the Shinji that is being written about in this fanfiction not the rebuild, EOE or series one.

I'm looking forward to this Chapter...

Excerpt from Episode IV: The Last Hope – Chapter 6 – Operation Yashima; Ramiel Obliterates

It had been a few hours since Shinji’s new friends had left. Toji, Kensuke and Hikari stayed for a while. They ate, they talked, and they watched some TV. Shinji was happy for the first time since he could remember, since the last time he made a friend in Tokyo–3 almost 11 years ago. However, Shinji was still tired from his runaway attempt, and his stint of being unconscious (courtesy of Section 2), as he hadn’t really slept that well since the night before he fought Shamshel.

Misato was sitting on the couch next to a nearly passed out Shinji, and she got a phone call.

Brrring… brrring… brrring…

Misato took a sip of beer and answered the phone. “Hello?”

“Hey, Misato. Can you come down to the cleanup site? I know you’re busy getting over Shinji leaving…” Ritsuko said.

“He didn’t leave, Ritsuko, he’s right next to me.” Misato said proudly. “He decided to stay and pilot.”

“Oh, really? I’m surprised… I didn’t think he’d pilot again. What changed his mind?” Ritsuko replied. “You didn’t bribe him with your body, did you?”

“I’m not a sexual predator Ritsuko, so leave it alone!” Misato shouted. “He stayed because of some people he met at school. They were worried about him.” Misato sighed. “So, why do you need me at the cleanup site exactly?”

“Well, I need you to come and look at this Angel and the data we’re getting about it, you might find it interesting.” Ritsuko replied. “And, bring Shinji too. He should see how his hard work pays off.”

“Yeah, I’ll wake him up and we’ll be there in an hour or so, ok?” Misato said looking over at Shinji’s sleeping form.

“Sounds like a plan, Misato.” Ritsuko said. “See you soon.”

Misato put the phone down and shook Shinji gently until he stirred and moaned in disgust. “Hey, Shinji? Wanna go for a drive? You’ll get to wear a cute helmet.”

“Just want… sleep…” Shinji replied tiredly.

“Oh, don’t be such a spoil sport.” Misato said, shaking him more. “You’ll love it, I promise.”

“Fine…” Shinji muttered. “As long as I can nap in the car…”
–––

Excerpt from Episode IV: The Last Hope – Chapter 6 – Operation Yashima; Ramiel Obliterates

Shinji was sitting outside Rei’s apartment, waiting for her to walk out, and trying to relax after what had just happened.

‘Man, I really made an ass of myself in there, I’m such an idiot.’ Shinji thought sadly. ‘She must hate me for… touching her like that.’

Rei walked by and glanced over at Shinji. She paused to stare blankly at him, and then continued walking along to her destination. Shinji got up and ran after her.

“Ayanami!” Shinji called out. “Wait up!”

The two arrived at the train station, and rode to the entrance of NERV HQ in silence. They were both thinking silently while they rode down to the Geofront.

‘Why am I being so nervous around her?’ Shinji thought. ‘Are things going to be awkward now that I’ve seen her…’ Shinji shook his head. ‘No, I can’t think like that, I have to try and fix this. I just wanted to be her friend… just have to think of something to say.’

‘I wish Ikari would stop glancing over at me so much.’ Rei thought. ‘I am a person, but why are people always so afraid of me. I just do not understand people, perhaps Ikari’s behavior is perfectly normal, I would not know.’

The train pulled into the station, and Rei got up quietly and put her book away. When they got off the train, Shinji tried talking to Rei again.

“Today is your reactivation test with Unit–00, isn’t it?” Shinji asked. “Aren’t you scared of getting back into your EVA after what happened?”

“Why would I be scared?” Rei said.

“Because, your EVA could go berserk again, you could get hurt again, or die!” Shinji exclaimed. “It could happen during a fight with an Angel, and it would put people in danger.”

“I am replicable.” Rei said plainly. “But if you understand the EVA, it will do as you wish it to. But you must understand.”

“What do you mean?” Shinji asked. “How do you understand EVA?”

“You cannot be told how to understand EVA.” Rei replied, pausing to turn to Shinji. “You must find out what EVA is for yourself, and only then can you truly grasp and control EVA.” Rei looked right into Shinji’s eyes. “Are you scared of your EVA?” Rei turned and went onto the escalator to the entrance.

Shinji rushed after her and got on right behind her. “Of course I’m afraid. Its stranger not to be scared.” Shinji sighed. “It’s a giant machine that has a tendency to go insane and hurt the pilot, like what happened to me my first time inside it, and what happened to you…”

“Can’t you have faith in the Commander’s work?” Rei asked. “In your father’s work?”

“Never.” Shinji said sternly. “I could never trust anything he does, he left me alone when my mother died, when I needed him the most. He only works for himself, and he’s a selfish fuck who never loved anyone…”

Rei’s eyes narrowed and she turned around. ‘How dare you say that about papa, he loved me… did he not? He was always there for me, and he bought the first Rei that Mew, a sign of his love and affection… how dare you Ikari…’

SLAP

Rei turned back around silently. ‘Why… did I do that?’ Rei thought. ‘Did I just feel… anger… or was I hurt by what Ikari said? I just do not know… and I do not understand these emotions I’m having, they are very confusing. I wish they would go away again, as they are hard to control.’

Shinji just stood there in stunned silence. ‘Why did she slap me? Was Rei defending… my father? Why would she do that?’

–––

"Shinji, DODGE!!!!!!!!!!!" Piccolo shouted.

Bring on the angry misfits

Yui's

Lilith's