Inside NERV headquarters, the bridge staff was panicking. The initial horror of the EVA suffering such a grievous injury to its head was quickly replaced with fear as all communications with the unit were lost.
"Exterior brain case has been damaged! Extent of damage unknown!"
"We're having problems maintaining activation! The synchrograph is reversing direction and the pulses are flowing backwards!"
"Cut the circuit!"
"I can't! It isn't accepting any commands!"
"What about the pilot?" Misato wondered, as she looked at the lifesign monitors. They looked much like a tangled ball of string for a bit, and then flatlined.
"This ends now…" "Abort!" Misato shouted, making herself heard over the din. "Rescuing the pilot is our first priority! Eject the entry plug!"
"We can't… It's gone completely out of control!"
And then… Unit-01 reactivated, its remaining eye glowing an eerie green as its mouth struggled to open. A horrifying wordless cry rent the air as the EVA regained its footing and regenerated its left arm. As another cry issued forth with the intonation of a word but not the syllables of one, the berserk unit charged forwards towards its foe.
HEH HEH HEH… NOW THIS IS MORE LIKE IT. COME TO ME, AND MEET YOUR DOOM, PATHETIC LILIUM.
The bridge crew could only watch in horror as the EVA tore the Angel's AT field in half, tore off one of the many spines around the Angel's core, and proceeded to beat it into bloody submission.
Suddenly, the Angel's form shifted, and it flowed into a featureless ball around Unit-01's head. "Oh hell… it's going to self destruct!" Ritsuko shouted. And, indeed, it did. A massive explosion rent the air, as several city blocks were destroyed and a column of flame reached almost a mile into the air.
As the berserk Unit-01 emerged from the inferno, roared, and collapsed, the bridge crew let out an involuntary sigh of relief, even as they shuddered at what the EVA had just done.
--
"An unfamiliar ceiling..." was the first thought that entered his head when Shinji woke up, as the details of a dream about a maze faded away. "Where am I?" and "What happened?" soon followed. After that came "I'm hungry... thirsty too." He was, after all, a teenaged boy. He also hadn't had anything to eat since his breakfast on the day he got into the Eva... whenever that was.
With a groan, the young man stirred, noticing for the first time the IV that ran into his arm, as well as the EEG and EKG machines that beeped softly next to the bed he was in. In a chair to his right, a woman sat, reading some sort of magazine. Temporarily dazed by the light, he couldn't identify her; rather, she appeared as a female-shaped red and black blur. He groaned again and rubbed his eyes, which allowed him to finally recognize her.
"Mi...Misato-san?"
"Sh...Shinji!" she exclaimed with a smile, quickly hiding the magazine she was reading, but not before he caught a glimpse of an image of pale flesh and plastic. "I see you're awake."
"I noticed," Shinji replied wryly. "What happened?"
"I don't know the details, but your EVA went berserk. After it tore the Angel apart, it shut down, and you've been unconscious ever since."
"Ah... how long was I out?"
"Oh, about three days. But, the doctors will probably let you out of here once you're conscious. They couldn't find anything wrong with you, after all."
"That's good... especially since I'm hungry." he replied as he slowly sat up. This motion caused the sheets to slide down, and he noticed that he was in a hospital gown. This caused him to pale immediately. "Um... where are my clothes?"
Misato responded with an impish grin. "I'm sure they're around somewhere."
Unnoticed by either of them, a pair of red eyes watched from the depths of a ventilation shaft.
"Ikari-kun…"
--
Some time later, Shinji lay soaking in the bathtub. He didn't know why he had been assigned to live with her instead of with his father, but he wasn't about to complain. Aside from a rather unfortunate incident involving her pet penguin Pen Pen, a shower curtain and a box of toothpicks, she seemed rather nice..
"Misato Katsuragi… she's not a bad person. But while bathing might cleanse her mind, all of may bad memories find me while I bathe. Like Father… or Rei Ayanami."
--
Early the next morning, Shinji found himself zoning out at school during a lecture about Second Impact. He had a very hard time paying attention to it, especially since he had a feeling that it wasn't true. Sighing, he pillowed his head with his arms, and attempted to catch up on some sleep. He was constantly dreaming of a maze, and his nights were not as restful as he would have liked.
He was interrupted by a message on his laptop that asked, "Is it true that you are a pilot Y/N?"
"What?" he responded.
"Are you the pilot of Evangelion Unit-01?"
Sighing, he figured that he might as well answer truthfully. They'd find out eventually anyway, and he hadn't been told to keep it a secret. "Yes."
He expected for one, maybe two of his classmates to turn and look at him, maybe gasp in surprise. He wasn't prepared for the whole class to exclaim about it, or to have most of the female population of his class clustered around him, asking what it was like.
--
After school, Shinji found himself accosted by a tall boy in a black track suit, who punched him in the face.
"Sorry, but I have to beat you up. I need to work off my anger." He punctuated this statement with a right hook. "You put my sister in the hospital, and I can't let you get away with that." Another punch.
"I didn't pilot it by choice," Shinji muttered. This earned him another punch, and the other boy stalked off, his camera-wielding friend in tow. Groaning, he rolled over, and suddenly found Ayanami staring at him, her arm in a cast and her head bandaged.
"We have an emergency call," she said. "I'll go."