A/N If you already read the other version feel free to skip to like, Chapters 9-10-ish. That's where the changes are.
Everything on the BUS seemed pretty normal, or, at least as normal as it can be for people who live on a plane and investigate alien crap. The team had just received a new order from Director Fury: to investigate a strange machine found in the basement of an orphanage.
"So, Skye, we have some news for you…" Agent Phil Coulson, the leader of the team, began slowly.
"You sound nervous," Skye, the resident hacker, observed.
"We have to go back to Saint Agnes!" Leopold Fitz, the mechanic, blurted.
"What?" Skye hissed, her eyes narrowed threateningly.
"Well, Director Fury received a call from a nervous neighbor, who was curious about the kids being dazed, almost hypnotized. He went over to investigate, just to make sure everyone was okay, when he saw a blue light coming from underneath the basement door. What he found down there was… disturbing to say the least," Jemma Simmons, the biochemist, explained.
"What did he find? What did Sister Mary do to the kids?" Skye demanded.
"What makes you think it was Sister Mary?" Jemma asked curiously.
"Because she's a nightmare. She screams, kicks, and punches. If there's anyone there that would hurt us- them- it's her," Skye spat.
"Us?" Ward, Skye's S.O and the team specialist, put in.
"I corrected myself. I don't live there anymore. When do we leave, AC?" Skye asked, bracing herself.
"Now," Melinda May, the pilot, answered. "Wheels up in two! Everyone buckle up!" She called over her shoulder as she left to go to the cockpit.
"Lovely," Skye sighed. "Just lovely."
When they pulled up to the two story stone building, everyone on the team had to admit, they were curious. Not only about the 0-8-4, but also what Skye was like when she was a little girl, what her life was like. She wasn't by any means 'talkative' about her childhood, keeping everything pent up, like a robot.
"Let's get this over with," Skye muttered, getting out of the black car with the SHIELD logo on it. They were about to knock on the door, but it was opened right before Coulson knocked on the elderly woman's scowling face.
"Sorry," He apologized sheepishly.
"Who are- Mary Sue?" The woman demanded.
"Call me that, and I'll erase you from existence, literally and metaphorically, myself," Skye threatened.
"Oh dear heavens, what has she done now?" The woman asked, rubbing her temples.
"For once, despite being surrounded by government agents, I was in no way responsible for anything. You on the other hand," Skye replied, gesturing to her, "I can't speak for."
"Sorry to interrupt," Fitz coughed, not looking even remotely sorry, "but I believe introductions are in order?"
"Oh, yes. I am Sister Mary. What can I help you with?"
"We're with SHIELD, here to investigate the 0-8-4 that was discovered in your basement a few days ago," Coulson explained.
"Ah, yes, follow me. Mary Sue, there are some children that wish to see you again, for reasons unknown," Sister Mary said, ignoring Skye's glare and previous threat.
"If anything goes wrong, I'll be in the living room," Skye whispered. When they walked by and saw Skye enter, all the other kids looked at her like she was God, in pure awe and amazement.
"Skye!" A little girl screamed, running across the room and launching herself into the hacker's open arms, making her laugh as she picked her up and spun her around.
"Hey Lulu," Skye said, tickling the girl's stomach. Her team was shocked at the open display of affection. Skye wasn't a hugger, in fact, she hated any form of physical contact. The first time FitzSimmons tried to give her a high five she flinched. They all turned their focus back to the impatient nun. They all followed her into the basement, keeping their eyes trained on any possible threat.
"Here we are," Sister Mary announced when she stopped in front of another door. "This is where the man found it. The circumstances of which he found it however were… less than ideal."
"How so?" Coulson inquired.
"Well, before the police contacted you, they looked around. They found him, but he was… different. Didn't talk at all. He became mute. It was like he lost all communication skills. His mind, it almost regressed somehow."
"I beg your pardon?" Simmons said, trying to remain calm.
"I don't know how to explain it. It was God, punishing him."
"Er, punishing him for what?" Ward demanded.
"I do not know. That is between his lost soul and the Father." Sister Mary shrugged. "But I must warn you… we do not know how to stop it, therefore one of you may get hurt," She warned.
"Skye said you were a monster," Fitz mumbled.
"Yes, well… Mary Sue-"
"Skye, Sister. Her name is Skye," Coulson interrupted.
"Yes, Skye," she paused disdainfully, "she was never one to be controlled. She was never violent, but she was dangerous, so to speak."
"Skye?" Ward asked.
"Yes. She was unpredictable, running off or hiding. It was nearly impossible to know where she was the majority of the time. She was playing a never ending game of hide and seek."
"So that makes her dangerous?" Jemma frowned.
"Not that. I don't know what she went through, but there were periods of time where she lashed out at anyone who approached her. She would scream, never cry, though, even as an infant, and kick with all her power. For someone so small, she certainly had a lot of strength." She pursed her lips. "But this is not about Mary- Sorry, Skye," she corrected.
"You're right." Coulson agreed.
"What's not about me?" Skye asked, rounding the corner.
"How did you know where this was?" Sister Mary demanded.
"Well, you just said it yourself," Skye explained nonchalantly. "She was playing a never ending game of hide and seek," she repeated. "Where do you think I hid?"
"You hid in the basement? It was always off limits!"
"Yeah, I know. Why do you think I was down here?" Skye laughed.
"I hate you," Sister Mary replied.
"Okay, I believe now we should intercede before things escalate," Jemma interrupted.
"Right, sorry. Let's do this." Skye sighed. When they opened the door, they saw it: it was just a simple wooden box, closed tightly. Almost like a jewelry box, with the drawers and everything. But Skye noticed something as she approached it; it had designs on it, that were pulsing and glowing blue and white. "AC, this thing is- whoa!" The thing opened, revealing a ballerina statuette, dancing along to the music. Out of nowhere, a blinding white light shoots out of it, encasing Skye. When the light passed, everyone gasped. In Skye's place sat a small four year old girl, staring wide eyed at her surroundings. She blinked, shook her head, and turned around to face the shocked nun.
"Skye?"
"Sister, is it almost time for lunch?" She asked. Or at least that's what everyone thought she said, but it was hard to tell since it was barely above a whisper.
"Skye?" Coulson asked cautiously, recalling what Sister Mary had said earlier about Skye lashing out.
"Who are you?" She scowled.
"You don't remember us?" Jemma asked sadly.
"No. You look familiar, but it's all pretty vague." She whimpered. "Where's Sister Katherine?" She whispered.
"She's dead, Skye. I'm sorry." Sister Mary explained soothingly.
"Then where's Miles? What did you do to my best friend?" She glared accusingly.
"Miles?" Fitz asked Sister Mary curiously.
"When they were younger, Miles was her protector. A guardian angel, so to speak. What are you going to do with her?"
"We'll take her with us on the BUS. See what the Director has to say. In the meantime, FitzSimmons, do your thing," Coulson said.
"Box it. Right away, sir." Jemma agreed.
"Before you go, Agent Coulson, I believe I may have something helpful to you," Sister Mary said, gesturing him to follow.
"Sister, where is the lunchroom?" A little girl, no older than three, asked the nun.
"Sister Grace, would you come here?" Sister Mary called.
"Yes, Mother Superior?" Sister Grace, a woman in her early to mid twenties, asked cautiously as she approached.
"Would you please take the little one to the lunchroom. She's lost her way, it seems."
"Yes, Mother Superior," Sister Grace said, bowing her head respectfully.
"Come," Sister Mary resumed walking, leading him to her office. She began rummaging through a cabinet, before pulling out a thick manila folder.
"What is it?" Coulson asked.
"Her file. Every report, foster home, mental assessment, and doctor's appointment, it's all documented in that folder. She was always gifted with technology, most likely thanks to Miles, so we had to take precautions. With Skye, she could easily hack the system and erase everything by the age of seven," she explained. "Please, she is fragile and delicate. She is glass, she has already been cracked, to the point where she most likely cannot be mended. I'm disappointed and ashamed to admit it, but I myself may have added a few extra cracks. I was unkind to her, and now she is unfixable." She sighed before rounding the desk and walking up to him, taking his hands in her own, wrinkled and calloused. "Be careful. The little flower is delicate. Good luck, Agent Coulson. If necessary, we still have some old clothes she can wear for the time being."
"Thank you, Sister," Coulson said gratefully.
"But I warn you now, Agent Coulson: when it is bath time, she becomes a demon," she shivered. "I recommend to whatever poor soul is being punished to wear a bathing suit," The elderly woman advised.
"I'll keep that in mind."
"Everything you may need to care for her is in that folder. I send you off with one final warning: she is deathly afraid of the dark. Keep the light on, or she will turn into a caged dog. She needs sleep, something that she did not get much of in her youth, I'm afraid."
"Thank you, Sister," Coulson repeated.
"Sir, we're ready to go," Jemma informed him.
"Thank you-" Coulson was interrupted by little Skye thrashing in Agent May's arms. Standing next to him was Ward, holding an ice pack to his face.
"You weren't kidding when you said she had a good punch," he said to the wide eyed nun, grimacing.
"I was not," she agreed. She walked over to Agent May. "Good luck, little flower," she whispered, walking away. Skye stopped thrashing, and May sighed in relief. Instead, Skye just sniffed, trying to hold back tears.
"Where's Miles?" The scared little girl whimpered.
"We'll find him," Coulson promised.
"Okay."
"Do some research when we get back to the BUS, Simmons," Coulson whispered as he walked past the biochemist.
"Yes, sir." She nodded. Fitz slowed down so she could catch up to him, and they started whispering to each other, most likely theories about the white light, or sciencey things no one else, especially not Coulson, would understand.