Note: this chapter will be updated in time.
Chapter 1:
After Shinji gets off of Asuka (After trying to strangle her.), they have a talk about what has just transpired between the both of them. After that, they go out to search for food in the ocean , after spotting an undamaged fishing boat nearby. After a few minutes out at sea They're able to catch a net full of lobsters. However, Asuka notes that these type of lobsters look nothing like any known species recorded (that's because what' she's holding in her hands is actually Ebirah). Just then, their net is attacked and destroyed by serpent like creature (it's actually a juvenile Manda). The sea dragon then proceeds to slither it's head on the deck of the ship and attacks the duo (Shinji is paralyzed by it's whiskers in the scuffle). Suddenly a giant red aquatic reptile (Titanosaurus) jumps out of the sea, and snatches the sea dragon with its jaws (going over the sea craft in the process. Realizing they were in serious danger, Asuka runs into the ship, starts up the engine, grabs a spear, and runs back outside. Only to encounter the sight of the animal with it's extended and currently sniffing the still paralyzed Shinji (who was starring at the monster in pure terror). Asuka (believing the creature would eat Shinji) throws the spear into the animal's eye. However, all this does is provoke the monster.a small chase ensues, with Titanosaurus chasing the small fishing boat (however, because it isn't used to the new LCL infested water, the creature stops to cough out the blood of Lilith for a few seconds before continuing on). Just as it seems like the two former Eva pilot are gonna get away, the aquatic dinosaur rises from the water using it's legs, and assumes a more humanoid form. It then proceeds to fire it's "Sonic Waves" at the vessel, destroying it. Both Shinji and Asuka wake up back on the beach, and decide to travel to what remains of NERV HQ, and gather supplies for when everyone comes back. However, unbeknownst to our heroes, they are being watched and stalked by big, insect-like eyes.
Chapter 2:
On their way to NERV HQ, Shinji and Asuka stop by their old apartment (now in shambles, and is 23 feet in the ground) to collect some things before going on their journey. However, when they get there, they encounter a Human-sized Praying Mantis that is investigating it's new environment (a juvenile female Kamacuras). Like the lobsters, it looks nothing like any known species of praying mantis. Their able to subdue and drive off the creature. However, two days later, they are forced to vacate the area when the Kamacuras returned (bringing more of her kind with her). After that, continue their travel to the base (while on the way, raiding buildings for food). With the same insect creatures continuing to follow them (while hiding In the shadows). They are able to get to a secret access tunnel near the school. Surprisingly (aside from there being a thin, red fog, and the sky blocks being gone, revealing the sky above), the Geofront, lights, and Pyramid containing NERV HQ are strangely intact (though, the Pyramid is full of holes. Including a huge hole in part of the structure where the command center is located). However, when they get to the Pyramid structure , they are ambushed by the mysterious insect creatures (which are revealed to be a small swarm of "Meganulons"). Which proceed to chase our heroes into the remains of the facility. They manage to lose them in the dark hallways,and make their way to the command center. Upon getting there, they discover that the area has been turned into what appears to be a nest full of eggs (the nest is located where the projector screen used to be). After surveying the area. They are yet again attacked by the Meganulons. Only to be indirectly saved by a pair of red and brown pterosaurs (Rodans), which proceed to feast on the little prehistoric dragonflies. However, upon spotting the former Eva pilots, the mates go into a frenzy (the male Rodan chases both Shinji and Asuka out of the command center, while the female stays behind in order to protect her eggs.). The duo is chased though the hallways and into a corner. But just as the animal is able go in for the kill, it is jumped from behind, and gets stabbed in it's right eye by someone in the shadows. The animal screams in agony, and flees. When Shinji and Asuka look again, they both see that the figure is in fact "Misato Katsuragi", their guardian. Misato then grabs the two, and the three are able to escape to the outside.
Chapter 3:
After evacuating the abandoned facility, Misato explains that after coming back from Instrumentality, she had also decided to go back to NERV HQ to get supplies. She did try to stop by her apartment, only to find that it was infested with Kamacuras. After that,the former pilots then proceed to catch her up on what's currently transpired (including the eggs they found in the command center). Concluding that the Rodan and their offspring could be a serious problem for humanity when it returns, they hatch a plan to destroy both the pair and their eggs (though, Shinji is hesitant with going through with it). After coming across a still functioning tank that was used during the JSSDF's assault on NERV, they return to the base, and attack the male Rodan (who is guarding it's new nest from any intruders). After a long skirmish, they are about take down and kill the animal. Sensing that her mate had just been killed, the Female launches out the side of the building and straight at the armored transport, intent on avenging it's mate's death. While it's successful in destroying the tank, it is in vain, as it gets a grenade thrown into it's mouth, killing it from within. After this, the three then enter one of the hole in the pyramid, and ascend the stairs to the command center. But their too late. Not only have the eggs hatched, but the offspring seem to have flown to parts unknown. With their problems seemingly gotten worse, the three pack up as much stuff as they can, find an exit from the Geofront, and promptly get the hell out of dodge. However, unbeknownst to them, a single Meganulon managed to survived the Rodan's assault. And (with no one to stop it) sends out a signal to the hive, alerting them that it has found a new nest.
Chapter 4:
As the three travel through what ruins of Tokyo 3, both teenagers asked Misato where they're going. In which she tells them that they are going back to her apartment. When they asked why exactly, her response is"If you think that I'm just gonna let a bunch of Gi-Mantide take my property for themselves, then you'd sadly mistaken.". Both teenagers simply looked at each other. After some time, finally arrived at the remains of the apartment, only to find the place abandoned (not even any Kamacuras could be seen, or heard). Too tired after the fight with the Rodans to do anything, the three decide to lay down and get some rest. However, a few hours later, Shinji wakes up to the sound of what appears to be hissing that coming from the door. When he walked over and looked through the peephole to see where the sound was coming from, he was greeted by the image of a lone Kamacuras standing outside. With this in mind, he quickly (and quietly) makes his way over to Misato and Asuka (who were asleep on what was left of the couches, together), puts his hands over their mouths to wake them, motions them to be quiet, and lip syncs the words "It's back", letting them know that the creature was right at the door. The Kamacuras (having smelled the humans inside) begins banging at the door with it's claws. Without hesitation, Misato runs up to the door, pulls open the door, and shoots the mantis in it's eye with her pistol. This causes the creature to writhe in agony, before fleeing. Misato then orders Shinji and Asuka to find whatever they can outside in order to board up the windows on the first floor. While they do that, Misato goes off to fish for food. She comes back with some strange looking crabs (Ganimes) she caught while fishing. After an hour of finding materials, and another boarding up the building, it's now nighttime. Misato was sleeping in her bedroom when suddenly, she hear a knock at her door. Upon opening it, she sees Shinji (starring right back her) when she groggily asks him what's he's doing, Shinji answers by saying that he had come to apologize. Confused, Misato asks what is their apologize for. Shinji's only response is "Fir failing to save Asuka, and causing Third Impact." Shocked, Misato tells him that what happened that day was not his fault, and was instead under the heels of both his father, and SEELE. Shinji (with tears starting to form in his eyes) then brings up what she said to him before her death-
"If you don't do anything right now, I won't Ever forgive you!"
And not only had he done just that when Asuka was fighting the Mass Produced Evas, but it was his decision to in-act Instrumentality. However, Misato counterpoints, stating that there was nothing he could done to break the Bakelite that entrapped Unit-01 at the time. And while yes, it was his decision to in-act Instrumentality, it was also his decision to reject it. And if it weren't for that, she, Shinji, and Asuka wouldn't be back on this small, red planet they call "home". After hearing that, all Shinji can do is hug his mother-figure. Misato tells him he should get some sleep, and that he'll feel much better in the morning. She then walks him back to his room, tucks him in, and promptly tells him "Goodnight". And with that, The Third Child drifts off to sleep.