Somewhere in Heaven

"Ah hah! Here's the problem. The last idiot who manned this multiversal control station had the damn common sense function for the sapient lifeforms set to off."

"Really? Well, no wonder this particular damn multiverse got stuck in a time loop! Wait...shouldn't the last guy who had my job have noticed that the setting was off? And for that matter whatever happened to the guy who was supposed to be in charge of this multiverse anyway?"

"Not sure... but I heard a rumor he got bored and fucked off to some other reality. I've already sent a message up to the BIG Boss though and after he gets around to reading it I guarantee you he's hunting that flake down and giving him a permanent reassignment as a latrine cleaner in one of the hell dimensions."

"Yeesh! Glad I'm not him. So anyways we throw the switch and what happens? Instant boost to the mortal's common sense levels?"

"Yeah but since time in each timeline moves at a slightly different pace from one another the changes aren't going to occur at the same exact point in their history. The good news though is we can watch all the changes from here!"

"So it's like getting to watch a whole Netflix anthology of what-if stories in one go?"

"Yup"

"Cool! Well, don't just stand there man, throw the switch!"

Timeline 1: Ritsuko

'Did he seriously just ask me to go naked in front of the council and expect me to still keep doing his dirty work?... you know what, now that I think about it maybe pining after a guy who keeps clones of his dead wife around isn't too bright. Time to make some backup plans!'

Sometime later:

*Bang!* *Bang!*

"Ritsuko! What the actual fuck?! Why did you just shoot the commander and sub-commander in the back of the head?!"

"Because Misato they were planning on killing us and then everyone else on the planet."

"...what?"

"Yeah...it's a loooooong story. If you want to hear it then I suggest you get an ambulance to load up Asuka and take us and Shinji FAR AWAY from Tokyo 3 ASAP."

"...why?"

"Because when the delayed countdown I programmed into the Magi goes off all of NERV's dirty secrets are getting dumped on the internet... and then the Geofront's nuclear self-destruct will go off."

"WHAT?!"

"And before you try to get Maya to bypass it please remember that she's good but not me and I've already changed all the codes. So yeah TICK TOCK time is a-wasting!"

Realizing the truth of what her seemingly insane friend was saying Misato quickly triggered the evacuation alarm for the city. Fortunately, after Rei 2 previously blew herself up Tokyo 3 was mostly abandoned as its prior inhabitants had become sick of having the rates on their insurance for Kaiju-related attacks constantly going up. As a result, when the evacuation siren sounded it didn't take long to get the remaining people out of there. By the time Selee realized what the hell was going on the nuke had already detonated and vaporized the remains of Gendo, Adam, Lilith, and the two remaining Evas who without pilots had no AT Field to protect themselves from the explosion. Without Adam or Lilith or the Lilith-based Unit 01, and with the damn Lance of Longinus currently stuck in space around the moon there was no way for Selee to initiate Instrumentality...not that they would have had the opportunity to do so even if that wasn't the case, as the second the classified files got dumped onto the internet EVERYONE and their mother who wasn't a part of the conspiracy and had lost someone in Second Impact had almost immediately stormed the UN, the homes of the Instrumentality council, and their local government offices and lynched everyone listed in the files.

Timeline 2: Fuyutsuki

'Wait a damn minute why the hell am I trying to bring back a woman who I know doesn't want to come back, who never showed any romantic interest in me, and who probably will hate my ass for not helping her kid in any way? What am I, some kind of retard?!'

Subsequently, the second Tabris got killed and the Evas were no longer needed Fuyutsuki shot Gendo. By that point though Ritsuko had finally given up on Gendo's creepy yandere ass meaning nobody gave a shit he was dead. Plus even if they had, once everything about Instrumentality was explained to everyone else on the staff they agreed it was the right call. Then they proceeded to dump all the Magi's classified info on the internet and triggered the base self-destruct system.

Timeline 3: Misato

"So Kaji you're saying that the reason you know this thing is Adam...is because you PERSONALLY GAVE ADAM to Gendo?"

"Well I was trying to maintain my cover as a double agent and...wait where are you...?"

"Fuck this nonsense! We are DONE Kaji! There's no way in hell I can stay with someone as dumb as you!"

Misato promptly marched into the commander's office under the guise of reporting a security breach and double-tapped Gendo before he could call for help. Not wanting to die Fuyutsuki subsequently revealed the whole conspiracy. Adam's embryo was promptly chucked into the base incinerator which instantly stopped the arrival of any future Angels as they could no longer hear their father's call. Kaji and Ritsuko both grief-stricken over the dumping by/death of their significant other ended up hooking up and after realizing what they had wasn't too bad they helped Misato upload all of Nerv's files onto the internet before triggering the city's evacuation warning and self-destruct sequence to destroy the Evas and Lilith.

Timeline 4: Asuka

"Misato..."

"Yes Asuka?"

"I refuse to go along with this plan."

"What?! Why?"

"Because it's fucking stupid and suicidal and this whole thing is probably a trap staged by the Angel! Also, I refuse to have my Unit 02 get dressed in that ridiculous-looking heat-resistant suit, and last I checked, no second child no functioning Unit 02! Not to mention I know for a fact that we have plenty of Angel DNA samples to work from making this whole plan completely unnecessary! Didn't that idiot Shinji leave you an entire angel corpse to examine previously?!"

"...but what about taking the fight to the Angels for once?"

"Just stuff the damn suit with some nukes and lower it down to where the Angel is. If they're anything like the Evas then an inactive and sleeping angel probably doesn't have an AT Field."

"But that would set off the volcano!"

"Yeah...but the Angel's probably going to do that anyway once it wakes up."

"...huh"

Sandalphon was promptly destroyed without any unnecessary heroics.

Timeline 5: Jet Alone

"Tokita you're fired"

"What?! Why?!"

"Because building a giant robot to fight giant nuke-proof monsters without weapons of at least equal magnitude to said nukes, and having said robot be equipped with coolant rods that stick outside its body in an easily grabbable manner when we know for a fact its proposed opponents have so far tended to favor melee assaults is by far the most IDIOTIC thing I have ever heard, not to mention a giant fucking waste of money!"

Tokita was subsequently fired and the resources that would have gone to build Jet Alone were instead sent to NERV without the need for them to arrange any sabotage.

Timeline 6: Gendo

'Oh no, Rei! I need to get down there and...wait a damn minute why the hell am I willing to risk my life or waste time waiting for Rei to recover when I can just revive another one of her clones?'

After the recovery team pulled her near-dead body out of her entry plug Gendo discreetly let Rei 2 die in the hospital and activated Rei 3. Rei 3 then promptly used Unit 01 to kill Sachiel. As a result, Gendo never bothered to contact Shinji and instead arranged for the Second Child to come to Tokyo 3 sooner. He later arranged for a certain idiot kid by the name of Aida (who was constantly trying to sneak into the Geofront to see the big robot) to pilot Unit 0 since he needed a third pilot (and also because dealing with the kid's break-in attempts was fucking annoying). Aida subsequently blew himself up instead of Rei against the 16th angel. Unexpectedly just after the last angel was killed Rei 3 having secretly nursed a grudge over Gendo not saving her sister would kill the commander by stomping on him with Unit 01. She then promptly told the rest of Nerv the commander's plans and they blew the damn base up.

Timeline 7: Gendo AGAIN

'...yeah maybe I shouldn't go and abandon my damn kid like my own folks did to me. Especially since even if I succeed and bring her back, then Yui will probably kill me for abandoning him!'

Gendo thusly didn't abandon Shinji. After Rei was accidentally created in his attempt to bring Yui back Gendo ended up adopting her. He later politely told Naoko he wasn't interested and after a small bit of binge drinking she and Fuyutsuki hooked up. Eventually spending time with his kids convinced Gendo that life was worth living without Yui and he ratted out the Selee council. Later when visiting Fuyutski and Naoko he ended up meeting and getting interested in Ritsuko and they started a relationship. Naoko, having grown happy in her relationship with Fuyutsuki, and eager to get some grandkids, decided to let her jealousy over her daughter snagging her former crush go so her daughter could be happy too.

Timeline 8: Adam

'Wait...so I overslept and there's already life on this planet? ...Ok then!'

Adam promptly used his godlike powers to teleport over to Mars and started up angelic life there. With no Angels on Earth to fight Selee's plans for Instrumentality fell apart and so the former masterminds of the cabal instead decided to spend their days idling away their money on hookers and pure Columbian blow. Neither GEHIRN nor its successor organization NERV formed and so all the people that would have been affected by second Impact's nonsense ended up living relatively normal lives...except Rei...what with her not having been...you know, born and all.

THE (MOSTLY HAPPY) END!