This is a fic I had been working on since...hell, around half to a decade ago now after having my mind destroyed by 'The End of Evangelion'.
The idea being basically that Shinji decides in Third Impact to 'go back', but Lilith takes a different idea of what 'go back' means, inserts a steel rod into his back to make up for his complete lack of a spine in the OT, then sends him back into the past. Angst mostly intact, but with full knowledge of the future and the ability to actually stand up for himself (shock horror!).
Also, as a side-effect from Instrumentality, Shinji went back to the past with not only his own knowledge and memories, but also those of the people around him. For example, he has Asuka's memories of when her mother went crazy, knows the rather intimate (and private) details of Kaji and Misato's history (and a couple things that Kaji never told anyone), and full knowledge about the true events of the Second Impact.
The Atoner: Shinji. Misato -and Hikari- can not understand why he seems so determined to make everybody happy. They can not understand it because neither of them knows he blames himself for everybody's deaths and for letting everybody down.
Batman Gambit: Shinji is trying to master the technique. He is using his TI-knowledge to goad people into doing things. One example was telling Asuka his mother was dead. He hoped she would ask how Yui died, giving him a chance to hint to her that they were Not So Different. His plan succeeded.
Battle Couple: Asuka and Shinji started on the path to becoming one as of battling the Sixth and Seventh.
Bond One-Liner: After defeating Shamshel, Shinji internally muses that one of the advantages of time travel is the ability to use all the quips he came up with too late.
Break the Haughty: Subversion invoked. Shortly after meeting Asuka for first time -again-, he feels tempted to bring her down a notch... but he will do not it, not matter how overbearing she may be, because he has seen what would happen if her pride was shattered, and he has absolutely no desire of seeing it happening ever again (could possibly count as a deconstruction).
Broken Ace: Shinji again. Comes across as The Ace to the rest of the characters, but deep down he's fighting hard to keep himself from falling into old habits; add to that the massive amount of guilt and self-loathing he feels towards his actions in the original timeline.
Brother-Sister Incest: Shinji has decided he will romantically pursue Asuka and treat Rei like a sister this time around. However he also thinks his feelings towards Rei are so deep like his feelings towards Asuka. He also finds Rei physically attractive, and sometimes he had to reminding himself she is his sister.
Canon Immigrant: Someone asked the author if Mana Kirishima would show up. He answered: "Who is Mana Kirishima?". After looking for information about her, he stated she would show up, but nobody better count on it being more than one scene or her role being big.
Can't Live with Them, Can't Live without Them: While sleeping for first time -again- in Misato's house, Shinji recalls that once he had begging for someone -anyone- getting Asuka out of Misato's house... and now he feels terribly alone without her, he misses her and he needs her.
Can't Spit It Out: There are two things Shinji can't spit out to Asuka: his feelings towards her (because he is certain of she'll run for the hills if he confesses too soon); and the bit about him being a time-traveler and being awfully sorry for all that he did and did not do to her (because her life and safety depends on him keeping his mouth closed).
Cassandra Truth: Fully knowing how it went the previous time, Shinji tries to point out the obvious risks in the mission for capturing the 8th Angel. This causes Asuka (who was mad at him at the time) to laugh in his face and go along with it anyway. Of course, when the mission turns to disaster the way he predicted and Asuka nearly ends up killed as a result, she feels guilty for dismissing him so lightly.
Clingy Jealous Girl: If someone asks Asuka, she will tell Shinji is a friend... but if another girl suggests she'll get her hands on him, Asuka will warn her away. Hostilely. Likewise, Rei does not appreciate her female schoolmates' obsession with Shinji.
The Chessmaster: Gendo and SEELE of course, but in this fic they are joined (and opposed) by Original character Major General Shigeru Ishiba, the Director of the Japanese Defense Agency (Intelligence).
Shinji is trying to become one, too. He is trying to outmaneouvering Gendo and SEELE using knowledge what they do not know he has. Time will tell if he is sucessful.
Childhood Friend Romance: A NERV officer reveals Shinji, Asuka and he had met once when the first two were toddlers... and they already fought back then. Shinji finds it amusingly ironic but disturbing. Asuka finds it hilarious.
Combat Pragmatist: Before battling Israfel, Asuka mutters "Two against one is hardly a fair fight." Misato sharply informs her the last thing she wants to give the Angels is a fair fight. Shinji is not particularly concerned with fighting fairly either (and in fact he has a quite the unfair advantage over the enemy, which he exploits wantonly).
Cool Down Hug: Shinji did to this to Asuka unawarely (or rather, Asuka thought he was unaware. In a nutshell, she was suffering of nightmares, and right like in the original series, she slept with him. It worked, and she managed sleeping peacefully... But she only thought he was sleeping. He was wide awake... and afraid of getting murdered if she noticed). Later Asuka realized he had trouble sleeping, and decided repaying the favor: she ordered him moving over, lay down on his bed and she slept with him.
Deadpan Snarker: Because of his former life and his new confident attitude, Shinji has developed a very sarcastic, caustic sense of humor.
Dead Fic: The lack of updates in two years suggested it had become this, but the author has assured readers he is still working on it — and in 2011 posted new material to prove it.
Driven to Suicide: Mentioned, but not really invoked. After Shinji reveals his whole story to him, Kaji wonders how the kid has kept himself from "eating the gun", so to speak.
Drives Like Crazy: Shinji is fairly convinced Misato learned her insane style of driving from Kaji. At one point Shinji suspects he actually broke a few laws of causality while parking.
Dude, She's Like, in a Coma!: When Shinji thinks about what he did the only time he saw Asuka naked, he disgustedly wonders what he was thinking.
Emotionless Girl: Rei begins like this but she slowly starts opening up. However she decides to hide her changes from Gendo and SEELE out of a growing sense of self-preservation.
Falling into the Cockpit: Subverted. Gendo and everyone else believe Shinji is piloting EVA for first time. He is not, but he successfully deceives them.
Fiery Redhead: Asuka is quite the spitfire, although Shinji's influence is subtly helping her to control and channel her temper better.
Forgiveness: Shinji seeks everybody's forgiveness by not screwing up things this time, even if no one remembers what he did.
Forgotten First Meeting: In chapter 9 a technichian told him Shinji that Asuka and he had already met when they were toddlers (something both of them had utterly forgotten about). Asuka's mother was visiting the Japanese Branch and left both in a play pen, and they... well, they fought. Shinji got a good laugh of it (thinking that some things never change), and so Asuka did when he retold her the episode to her.
Gender Flipped: Shinji, Touji and Kensuke call -very privately and very quietly- Asuka, Rei and Hikari "The Three Stoogettes".
Genre Savvy: It's funny how much insight time travel gives:
In his rather extensive experience on the matter, brooding in a bedroom for that long just never led to good things.
Guile Hero: Played straight with Kaji, subverted with Shinji. After a meeting with Seele goes awry, the former warns the latter he must not try to play the trope because he is not trained for it.
Heroes Want Redheads: Shinji. He blatantly admits Asuka is the only person he would have gone to the school dance with.
HeroicBSOD: Shinji has a near mental breakdown in chapter 13 when he's recounting his story to Kaji and a JDF intelligence officer; they have to slip him a mild sedative to calm him down.
Hope Is Scary: Shinji is managing to prove to Asuka for first time in ten years she has met someone she can trust and rely on. She thinks maybe Shinji is someone she does not need to push away, and she can lower her walls around him... and the thought scares her more than any Angel.
Just Friends: During the school dance, a girl asks Asuka if Shinji and her are an item. Asuka replies they are just friends. Of course, when the girl suggests maybe she will get him all for herself, Asuka advises her keeping her hands far, far away Shinji.
Knight in Sour Armor: Poor Shinji. It isn't that he doesn't want to help, it's that he feels extremely morally obligated to help.
I Need a Freaking Drink: A hilarious version. Shinji, on a whim, reveals the whole bit about "I'm a time traveler who's trying to change the past to atone for my mistakes"... to PenPen. The bird's response?
(PenPen) stared at his back for several long, long seconds before continuing into the kitchen, retrieving a can from Misato's stash, stopping in consideration, retrieving a second, and retreating into his fridge.
"Yeah" Shinji muttered as he stacked the plates in the dishwasher. "That's about what I thought you'd say".
Played straight with Kaji, who admits he needed several hours of hard drinking after getting proof of Shinji's claims of time-travel.
Ironic Echo: Asuka to Shinji: "You're not the type of person who just sits around, moping in your bedroom for hours on end."
Leeroy Jenkins: In her second battle, Asuka carelessly charges head-on, ignoring Shinji's warnings. Thank Shinji she avoided getting her butt handed to her, but she still acknowledged and cursed her own recklessness.
Let's Get Dangerous: Shinji's new attitude is due to him being aware of what is at stake and refusing to fail everybody again. Hence, he is more determined and dangerous in battle.
Manipulative Bastard: Koga Hayashi, the JSSDF's top Interrogator; known as "The Warlock" behind his back. However, he's arguably one of the good guys.
Mama Bear: When Shinji and Asuka were fighting Gaghiel Shinji could not focus properly. Then he tried reaching out for Asuka's mother, screaming mentally her daughter would die if she didn't help them. Kyoko reacted so furiously the backlash knocked Shinji out, as Unit-02 easily forced Gaghiel's jaws open. Asuka reached a 100% synchronization with her EVA right then. Misato is also fiercely protective of Shinji and Asuka (Kaji notes that she was perfectly willing to kill to protect Shinji.)
Meaningful Name: Averted. We get to see things from the JSSDF's POV this time around, and the Code Names they use are deliberately meaningless; the guy actually responsible for the designations tends to name them after random, everyday things that happened to be nearby. Example: Operation "Wallpaper" is the name for their highly classified ongoing investigation into SEELE and NERV, while their highest ranking source is known as Agent "Balcony".
A lot of things PenPen does tends to mess with Shinji's or Asuka's mind; Misato has somehow turned the bird into an alcoholic and he apparently reads the Wall Street Journal every morning to check stock rates.
The Mole: Shinji. He reveals the truth to Kaji, hoping the older man and spy will help him to avert the Third Impact. In turn, Kaji gets him in contact with the Military, and he (Shinji) becomes their best source of info on the activities and goals of NERV and SEELE. He even gets a code-name: Balcony.
Reverse Mole: He mixes both tropes. On one hand, he is feeding information to the enemy about what the organization he works for he is up to. On the other hand, given WHAT that organization is up to, and what he is trying to avert (including the deaths of those ones he cares for), you would be hard-pressed to call him a bad guy (and if they knew about his motives, it is highly doubtful anybody bar Gendo and SEELE would call him a traitor). He is essentially a good guy pretends to be a bad guy pretending to be a good guy.
No Endor Holocaust: Averted. The author doesn't shy away of showing how much people perish in the battles and how much collateral and property damage they cause.
No-Holds-Barred Beatdown: Shinji's return match against Sachiel. After ultimately deciding against waiting for Unit-01 to go berserk on its own, he takes advantage of his previous synch ratio and combat experience to literaly tear the Angel down, leaving it almost no chance to retaliate. He even manages to contain the blast caused by its self-destruction with his AT-Field, and acts confused after the fight to pass his combat prowess off as Unit-01's awakening.
After Shinji turned Chihiro down, some students spread rumors of he was gay. However, thanks Toji and Hikari, after a very embarassing morning, almost nobody believed those rumors. Shinji did not specify what happened in that morning.
Fuyutsuki does not know how the UN brought a frigate all the way in the Geofront, but he has not tried finding out to test his self-control... and he reasons it can not beat the history of the motorboat in Terminal Dogma anyways.
Not What It Looks Like: In a chapter, Misato caughts Asuka leaving Shinjis' room at the morning. Asuka has to explain that is not what it looks like, she had been not acting untoward towards Shinji and had a good reason for she sleeping in his room. And in his bed. With him in said bed, at the same time. The reason beuing he had nightmares and she was triyng comforting him.
Obfuscating Stupidity: Genre Savvy Shinji goes out of his way to act completely inept in his first combat simulation (and does such a good job of it that the staff nicknamed him "Godzilla''), then asks for a week of training combat training so he can have a more believable explanation for his piloting skills.
From Gendo and Ritsuko when Shinji stated he remembered how his mother died. Also, Shinji realizing that one of the changes in the timeline was that the Angels were becoming more powerful and more dangerous than he remembered.
And from Shinji when he realized he had let Keel have a good glimpse of his thoughts.
And from the audience when Keel realized the Third Child somehow knew him.
One-Liner: Lampshaded. Shinji notes to himself that one of the best parts of going back in time is "Using all those clever lines you thought up too late."
Out-of-Character Moment: Like many Peggy Sue fics, this comes into play. Several characters have noted that Shinji's current personality does not match up with previous reports on him. Also, Ritsuko became suspicious of Shinji after she noticed the supposedly "Berserk" EVA 01 use a prog knife the same way she had seen Asuka do in a video report even though Shinji and Asuka had yet to meet.
OOC Is Serious Business: In chapter 10, Asuka admits that she had screwed up in front of Rei, and Rei apologized for Asuka. And Shinji, who was staring at shock and whose jaw almost hit the floor, wondered why nobody had informed him that Earth started rotating from West to East overnight.
Properly Paranoid: Shinji got forced to confront Seele in chapter 17. Inwardly he was coming up with all kind of bad scenarios and disastrous outcomes (including Seele saying they knew everything before putting a bullet in his head). His paranoia was, of course, justified and understandable. However, he never imagined what trump card Keel would play.
Red Oni, Blue Oni: Shinji and Asuka are like this. Asuka and Rei also are, but their relationship is mellower than it was in the original timeline.
She Is Not My Girlfriend: A girl asks Asuka if Shinji is her boyfriend. Asuka claims they are Just Friends, and the girl hints maybe she will take him all for herself, then. Asuka chewed her head off.
Shipper on Deck: Shinji tries hooking up Touji and Hikari. He also tries setting Rei up with Kensuke. Kaji also gives tips to Shinji for winning Asuka over. There also is an interesting inversion: Obviously Shinji is not against Kaji and Misato hooking up, but after telling Kaji how his death left Misato devastated in the original timeline, Kaji decides to stop flirting with her until the Angels, Gendo and SEELE are defeated and dead.
The Stations of the Canon: Inevitably due to it being a Peggy Sue fic, it goes throughout the series (Shinji coming Tokyo-3, Misato picking him up, he arguing with his father in the cages...), making gradual changes (for example, he did not run away after the battle against Samshel).
Tsundere: Asuka, of course. Though she's beginning to show more of her "dere" side than she ever did in Canon; due to her interations with Shinji, she's started to re-examine her life.
Tragic Keepsake: Shinji somehow brought Misato's cross-shaped pendant with him to the past (likely Lilith/Rei's doing) as a reminder of his past mistakes. Becomes important later on when it's used to prove his time-travel story to Kaji and the military.
WAFF: During the scenes involving Shinji and Asuka.
What Happened to the Mouse?: Some fans have wondered what happened to Rei/Lilith after her last chat with Shinji. The author has stated she was barely a memory that has since faded.
"So I'll make you a deal Third Child, [...] If you, at some point in the future, let me down utterly, completely and catastrophically like you think you might, I forgive you in advance for it…providing that you don't mope around like an idiot for the rest of your life but find a way, any way, to make it right, and you don't stop trying until you do. Fair enough?"