Author's Note: Hello, all! This is my first Halo fic, and it centers around a character who actually exists in the Halo universe, but is not mentioned. I decided to write out my own version of her, her adventure and fate in Halo, and her background, etc, and YES I have screwed with the Halo video game series storyline for all of this. This takes place in the first Halo game, Combat Evolved. Feel free to point out any errors in vocabulary or anything I get wrong that's from the Halo universe or books. I have read them, I just have trouble remembering what happened. Hint (just to make sure I don't kill anybody with the suspense and questions that would be going through their minds) the story title has something to do with this character's past.

My Unknown Loss

Chapter 1

"Em! Can you hear me?!" My head throbbed at the shouting voice. I groaned. I was in complete darkness, but where were the noises coming from? There was...gunfire, lots of gunfire. Shouts and yells were accompanying the gunfire as well. Was there a battle going on or something?

"Emily!" The voice shouted again. Who was it calling? I moaned.

"Is that...my name?" I heard the voice sigh.

"Your head hasn't recovered from that wound very well...You must have succumbed to amnesia." Blindly, I reached a hand up to touch my head, and I felt that it was very sore. I found what felt like a gouge, and my hand began to follow it, until it was grasped by a rough, callused palm. "Don't touch it. I'm going to bandage it again before I send you off." Instantly, I became scared at his words and I yelped,

"W-Wait! Who are you? Why are you sending me away? What did I do!?" Another callused hand gently picked up my right hand and held it. He sighed.

"Em, you didn't do anything wrong. It's just...your dad put you in my care, and I'm not willing to break the promise I made with him." My...dad? "I promised him that I would protect you, and now I'm going to send you someplace safe. Far away from the Covenant..." Covenant? The man sighed again. "I'm so sorry to leave you like this, Emily. I-I wasn't expecting you to get amnesia but...I wish there was something I could do..." I thought I could hear what sounded like sobbing, and it also sounded like it was being fought down. I heard an explosion in the background and the man cursed. "Alright, I'm done bandaging your head...I'm afraid this is goodbye, Emily." The hands left my side and I heard steam whooshing, like it was being pressured. I heard a large door close, most likely in front of me. I heard the man's voice again. "Be strong, Em!" I felt a large tremor shake my body, and I felt something around me shake. My stomach dropped when I felt like I was falling, and I did the only thing I could think of...I screamed, not hearing the ear-deafening explosion behind me.

* * *

John-117 calmly walked through the halls in the Pillar of Autumn, fully suited in his green MJOLNIR armor. He had just been called by Captain Keyes to the front of the ship, in the control room. He inwardly sighed. He was almost in one of the cryo-tubes when he was summoned. He'd much rather go into stasis than walk around in the ship, but still, duty calls. He took a glance at his gauntlets. His armor was pretty battered up from the battle on Reach.

John's eyes softened, turning his gaze to the floor. Reach, the planet he barely escaped before it was glassed by the Covenant, the planet where the rest of his SPARTANS were. He and two other SPARTANs were sent to wipe the data of Reach before the Covenant could get to it, and he lost those two in the process. Only he, Sgt. Johnson, and a few marines made it and escaped in the Pillar of Autumn, but as for the rest of the SPARTANs John left behind...They're....gone....He couldn't believe it, his brothers and sisters, all gone. SPARTANS weren't supposed to die. Now...I'm the only one left...John thought mournfully. Linda, Kelly, Sam, Fred, James, Will, Fhajad...all of them...He abruptly shook his head, shaking away his thoughts. Now wasn't the time, not when the Captain was waiting for him.

As he turned a corner, he pondered on what the reason why Captain Keyes called him could be. Maybe it's a briefing meeting...He pushed his thoughts when he approached the doors to the Pillar of Autumn's control room, which opened automatically with a beep once he got close. On the other side of the door was an large room with an enormous window in the front of the room, the dark yet beautiful vacuum of space just outside. Aligned with the room's wall were large computers, one man sitting at each one. In the very center of the room was a pillar with button pads on them and small monitor screens. John-117 walked around the pillar and began to walk to the front of the window. There was a large pit in front of the window, and down below the window curved and became a floor, just for those who wanted to stand down there and observe the view. In front of the pit was a long desk with holographic screens floating above it, a few men at the desk's seats, in front of each screen. A man with gray hair wearing a gray uniform was standing in front of the desk, watching planets and stars outside, his hands folded behind his back. John walked up and stopped once he was at least a couple of feet behind the man, and he saluted with his left hand.

"Master Chief Petty Officer Sierra-117, reporting for duty, sir," he announced just loud enough for the man to hear, his voice impassive and rough. The man turned and looked as if he was in his 50s. His hair was already grey and his eyes were a faded blue. On his grey uniform, right above his heart, were multiple ribbons. John knew that Keyes didn't get those for nothing, not from what he's heard. The Captain had a straight posture, and looked very strict in posture and facial features.

"At ease, Master Chief." John lowered his hand and Keyes held out his own, which he took and they shook hands. "It's good to have you on board, son." John nodded as they parted.

"Thank you, sir. Permission to ask a question, Captain?" Keyes raised a hand to stop the Chief's words.

"No need. I already know what you're going to ask. I called you up here so we can plan on what to do next." I knew it...John sighed inwardly-the cryo-tubes were going to have to wait. The Captain turned to a pole that was emerging from the ground, with a glowing ring embedded into the top. "Cortana? Care to explain to the Chief what you just told me?" The ring glowed brighter and there was a flash of small letter holograms, before a small, holographic, slender woman appeared on the pole. She looked like she was wearing a skin-tight bodysuit that covered her entire body, and she was made entirely of numbers and codes, scrolling through and around her body. She was glowing different shades of purple and blue and her hair was short, reaching just below her ears. The holographic woman placed a hand on her hip and looked to John.

"Good to see you, Chief." John nodded. "Alright, what I'm about to tell you won't come to be as much of a shock, but I'll say it anyway. When we jumped from Reach, we only jumped halfway through." Halfway? John thought incredulously and he asked,

"What about the Covenant? Weren't they following us?" Cortana shook her head.

"Honestly, I don't know. We could have lost them, or maybe they're still on our tracks, or perhaps they changed course." She lowered her arm. "All I know is that we should think of a plan, and fast, before they find us." Keyes nodded and turned to face the window again.

"We have a lot of wounded marines, and we lost many lives back there..." He stared in silence at the bright stars outside and he turned to Cortana. "Cortana, what's the closest UNSC carrier?" Cortana nodded.

"Just a moment..." She placed a hand on her temple and her eyes narrowed in thought, scanning. After a minute or two, she lowered her hand. "The closest one is not far from here, and one that managed to escape from Reach as well. It's the UNSC Atlas." Keyes raised an eyebrow.

"They got away? Hm..." He turned to the window again, hands folded behind his back once more. "Alright, Cortana, can you send them a message for permission to dock, and ask them what their status is?" Cortana nodded.

"Right ahead of you, Cap-" She cut herself off and placed a hand on her temple again, her features twisted in confusion and surprise. "...What in the...I can't believe it..." Keyes slightly turned his upper body to look back at her.

"What is it?" Cortana's brows knitted together, as if she was trying to make sense of something. John was becoming concerned by then; what did she see? Cortana sighed and lowered her hand before crossing her arms.

"You boys might want to take a look at this." She brought up a holographic screen and everyone in the room seemed to have brought their attention to it after seeing Cortana's confusion. The technicians began murmuring to each other about what was being shown to them while the Captain Keyes and John stared in confusion and suspicion. There, aimlessly floating not so far away from them, was a UNSC escape pod of some sort. Captain Keyes narrowed his eyes and turned to a couple of his technicians at their computers. His voice was stern as he ordered,

"Get me a reading from that pod, now. I want to know where it came from, what unit it belongs to, and if there's any sign of life on that thing." A few technicians nodded while the rest replied with a "yes, sir," before they began to type at inhuman speed on their computers. Meanwhile, John turned to Cortana.

"I don't get it. Why would there be an escape pod out here? We should be far away from Reach by now." Cortana could only sigh.

"I don't get it either, Chief. It might have gotten dragged along with us when we entered slipspace. Or maybe it was already here..." John gestured to the screen.

"Just drifting like that? Abandoned?" Cortana didn't reply and John began to feel uneasy at her silent answer.

"Captain!" They all turned to a technician in an orange jumpsuit and he looked to Captain Keyes. "I managed to get into its program and there's only one life form in that pod, sir." Keyes narrowed his eyes.

"Human or Covenant?" John didn't question why Keyes asked if there was a Covenant alien on board a human vessel. The things knew how to trick people, like the Elites. The tech looked at his screen before shaking his head, uncertain.

"I don't know, sir. But whatever it is, it's in pretty bad shape." Keyes raised an eyebrow and asked,

"How so?" Cortana raised her hand.

"Its head is severely damaged" She paused and shook her head in confusion. "Strange...it has a vital signs monitor. It's as if it just had medical treatment. Heartbeat is normal, and it seems to be asleep, or unconscious. I think it's in some sort of cryo-tube, in comatose perhaps." Keyes brought out his pipe, placed it in his mouth, and began to chew on it. He must be thinking about what to do, John thought. John stepped forward.

"...Captain?" After a few minutes of silence, Keyes lowered his pipe and turned to their AI.

"Cortana, give the orders for a pair of Pelicans to go out there and retrieve that pod." Cortana nodded as Keyes turned to John.

"Aye aye, sir." She disappeared in a flash of codes as Keyes said,

"Chief, you come with me. Let's go down to the hangar and see what we got." John nodded.

"Yes, sir." With that, Keyes turned and walked to the doors, with John following close behind. After a few minutes of walking in silence, they reached the elevator and entered before it began to descend. They were silent for a minute, until Keyes, with his back to John, began to speak,

"I...am very sorry about the other SPARTANs back on Reach, Chief. I understand how important and close they were to you." John was surprised; he never took Keyes as a man to sympathize, especially for SPARTANs. Keyes continued, "It wasn't only a loss for you, but for all of us. They won't be forgotten." John could only nod and mutter,

"Thank you, sir..." Keyes didn't reply and continued to stare out the elevator. After another minute or two, the elevator began to slow down and came to a stop. With a wheeze, the elevator doors opened and revealed two marines standing there, talking to each other. They froze once their eyes landed on John and the captain, and they both instantly saluted. Keyes nodded as he and John walked past them.

"At ease, marines." The marines lowered their hands and entered the elevator. Cortana's voice then entered the Intercom.

"Captain, the Pelicans have successfully retrieved the pod and it's now waiting for you in the docking bay. Sergeant Johnson and his marines are awaiting your orders for what to do with it." Keyes nodded as he kept walking.

"Thanks, Cortana. Tell Johnson and his team to wait until the Chief and I arrive. That is all."

"Yes, sir." After walking through numbered hallways and by many passing marines, Keyes and John had reached the entrance to the docking bay. The doors opened with a soft bling and a hiss of steam before they walked in.

They entered an enormous room, with ships of different sizes and large doors. Jeeps were parked in a nearby lot, each in their own aisle. Many marines in armor and gear were scattered about the place, either chatting with each other or doing what they were ordered. Sergeants were having their men go through drills and technicians were fixing the jeeps and vehicles.

"Captain!" Keyes and John turned to see an African-American sergeant approach them. John took note of the mustache and the Cuban cigar in the sergeant's mouth. Johnson. Sergeant Avery Johnson stopped and saluted the Captain before nodding to John.

"Chief, good to see you." John nodded back.

"Likewise." Keyes decided to get straight to business.

"So, you retrieved the pod?" Johnson nodded and gestured to two stationary ships behind his back with his thumb.

"Yep. But it's weird, sir." He looked down at the ground and shook his head, muttering, "I haven't seen a pod like that since a long time ago. Since around the beginning of the war, sir." Keyes raised an eyebrow.

"Are you saying that this pod has been able to keep something in cryo for over 25 years?" Johnson nodded and gestured for them to follow him.

"That's right, sir, but it looks like a model similar to the O.D.S.T SOEIV. The only thing that's different is that its interior is designed after an escape pod meant for one person only." Keyes nodded as he and John began to follow the sergeant to the Pelicans he gestured to, which were on the very far side of the bay. John noticed that Keyes had kept his hands locked behind his back the entire way to the bay.

"Can you see what's inside of it?" John asked. Johnson shook his head.

"No. It's as foggy as hell in there," he exclaimed softly. Keyes' eyes narrowed and he said nothing more. Soon they reached the Pelicans and they walked in between them, to find the pod that they spotted earlier laying on its back and a small group of marines standing around it, who all saluted once they saw their superiors. John realized as he stood next to it that it reached up to his stomach. If it were standing up right, it would be as tall as me...John pondered. Keyes walked around the pod and he placed his chin in his right hand as he examined it, his face looking grim.

"Cortana, can you open this thing?" he asked out loud. Cortana answered in one of the nearby speakers.

"Right away, Captain. It'll take just a minute...Aha! Got it." The pod's door began to spew steam pressure out of its creases and it hissed as it slowly slid in to its compartment at the bottom. Everyone could see through the window that the steam was fading and the inside was getting clearer. The door was finally fully open, and the steam faded more until they could clearly see inside. A faint beeping was heard, and it sounded like a heart monitor. Everyone froze in complete shock. Johnson grasped his cigar and pulled it out of his mouth, coughing up the parts of it he bit on out of shock.

"Wh-What the hell?" he choked out. All of the marines stepped back and one of them muttered,

"How in the world did she get out here?" The rest of them began muttering and John could only stare in shock behind his faceplate. There, sleeping peacefully in the cryo-tube, was a young teenage brunette girl. She was wearing a gray jacket, its flaps open, revealing her white t-shirt, and slightly tight jeans colored a faded blue. On her feet she wore a pair of white converse shoes. Her eyes were closed, her eyelashes twitching every now and then as she slept, and her mouth was slightly open, her breathing calm and deep. Keyes' eyes narrowed as he took out his pipe and began to chew on it again.

"Cortana, can you explain this?"

"Negative, Captain...I'm...I'm completely at a loss here, sir." Keyes frowned and turned to one of the marines.

"You, go get a team from the medical bay. Tell them we need a transport for an unconscious..." He glanced at the girl uneasily. "...guest of ours." The marine hesitated before giving a solid salute.

"Yes, sir!" The marine ran off and disappeared behind the hangar doors. Sergeant Johnson sighed as he placed his cigar back in his mouth, took a drag, and leaned over the girl, his elbow supporting him on the pod's edge.

"Damn...looks like a civilian," he uttered as he blew some smoke. John's eyes narrowed once he saw the smoke drift over the girl, and he walked up behind Johnson and gently, yet firmly at the same time, placed his hand on Johnson's shoulder.

"I think you should smoke somewhere else. We have no idea what this girl's conditions are..." Johnson only raised an eyebrow before removing his cigar, threw it to the floor and rubbed it out with his boot.

"I had enough anyways..." Johnson muttered as he resumed his position over the girl. Keyes crossed his arms as he stared at the girl.

"Why on earth would there be a civilian out in space?" John joined Johnson at the girl's side and he stared at her face. She looks like she's been through a lot...he mused. As he stared hard at the girl's face, he noticed a line of lighter skin on her forehead, barely visible beneath her brown bangs. John raised an eyebrow before reaching out his left hand to brush away her bangs to get a better look. The girl shifted her head a bit and she mumbled lightly, but went back to sleep. Nobody stopped him, Sergeant Johnson and Keyes only raised an eyebrow as they watched his movement. John withdrew his hand and gestured to the girl's forehead with it. Just as I thought...

"Look at that." All eyes followed where the Chief's hand was pointing and their eyes widened.

"Damn...that's one hell of a scar," Johnson muttered. Indeed, on the girl's forehead, just above the bridge of her nose, was a large scar in the shape of a slash mark, going diagonally down from the top right of her forehead to the bottom left, just next to her left eye. John's eyes narrowed.

"Looks like she got cut by something...We should-" He cut himself off once he saw the girl shift roughly in her position, and her eyes slowly fluttered open, to reveal confused, brown eyes.

* * *

Everything is so dark...Wait...Voices...I can hear voices...What are they talking about? Ugh...what is that smell? I felt something rough touch my forehead, moving my hair. What is this? Go away, I'm tired. I shifted a bit and relaxed again, but the voices were still there, talking. Who's there? I opened my eyes slowly, and I winced at the blinding light that meets them. I saw an African-American man and a huge green robot hovering over me, watching me. Wait, robot? My eyes widened and I abruptly sat up. Where am I? I frantically scanned the area, and I saw ships and men in grey battle armor. I gritted my teeth as a sharp pain stabbed my forehead and I grasped it with both hands, my eyes shut. I whimpered as another surge of pain struck and I managed to open my eyes a bit to the look for an exit. I have to get out of here! I shot up to my feet, stumbling a bit, and the men around me and the robot seemed shocked. The African-American approached me quickly.

"Hey! You sit back down, little missy!" he ordered in a stern voice. Another man, the one in gray, turned to the African-American angrily, shouting,

"Johnson, halt!" I stepped back away from this Johnson in fear and turned to leap down from whatever I was in, only to feel my legs buckle suddenly. Why do I feel so weak? I gasped and my eyes widened as I fell down several feet to the floor. I squeezed my eyes shut as I waited for my body to crash on the metal floor. The impact didn't come, and I felt myself get caught by two, stiff arms that felt like metal. I looked down and realized I was hovering a several feet above the ground. Confused and oddly dazed, I looked up to see my own face reflected in a golden mirror outlined with green. I sensed myself fading away again and my eyes slowly fluttered closed as I unconsciously whispered,

"My...dad..." Everything turned black...

* * *

John raised an eyebrow at the word he had just heard the mysterious girl in his hands whisper, barley underneath a soft breath. 'Dad?' So the kid has a family...He looked up at Keyes, whose eyes narrowed as he studied the girl.

"Seems we don't have an everyday citizen on board..." Johnson nodded in agreement.

"Yeah... and what the hell was that about?" John shook his head and replied,

"She was just shocked. She must have been unconscious for too long. We should get her to the infirmary... "He looked down at the comatose girl before glancing to Keyes. "Sir, with all due respect, I don't think we should wait for the medic you ordered for." Keyes walked up to him, pipe in his mouth as his eyes centered on the SPARTAN's visor.

"You have no argument from me, Chief." The captain turned to the Sgt. "Johnson, report to the Control Room. After we take our guest to the medical bay, we'll meet you up there." Johnson gave a sharp salute.

"Yes, sir." With that, the sergeant turned and left the hangar in an elevator shaft, as Keyes and John, who still had the girl in his arms, watched him leave. Keyes returned his gaze to the Master Chief, gesturing to a doorway with his head.

"Shall we?" John nodded once.

"Yes, sir." They both turned and walked alongside each other as they left the hangar, the girl dangling in the SPARTAN's arms as they walked.

Captain Keyes and SPARTAN 117 walked into the medical center and a woman in a white suit at the desk looked up in shock when she spotted the girl before she looked to Keyes.

"Is this the guest, Captain? We already sent a medic to the-"

"I apologize for that, Dr. Owens. We had a change of plans. She woke up in shock before she blacked out again." Dr. Owens' eyes softened as they rested on the young girl's form.

"Oh, the poor thing..." she uttered softly. She walked around the desk and gestured to a nearby hallway with her hand. "Please follow me." Keyes and John complied as they followed the doctor into the brightly lit hallway, stopped and waited for an automatic door to open, and walked after her into a vacant examination room. Dr. Owens stopped beside the examination cot and turned to Master Chief. "You can put her down on the cot, sir." John nodded and walked over to the cot, gently placing the young girl in his arms onto the straight bed, and watched as she slightly stirred with a moan before becoming quiet and still again. As he walked back to Keyes' side, the captain uttered to the doctor,

"She has a strange scar on her forehead. Do you think you can tell what happened to her?" Owens sighed as she began checking the girl's pulse on her wrist.

"It would be best if we just wait and give her time to adapt. I understand that if she was in shock, you all must have scared her to death." John noticed the annoyance in Keyes' eyes, but made no comment. Keyes walked up to Owens' side.

"We don't know if she's a trap sent by the Covenant or if she's an Insurrectionist. It's best that we know what she's doing out here in space." Dr. Owens narrowed her eyes and locked her gaze with the captain's.

"Would you think the same about your daughter, sir?" Keyes tensed and he looked down at the young girl's face, watching as she breathed softly in her sleep. His eyes softened as he watched her, images of his daughter flashing in the girl's place, and he felt tempted to reach out and hold her, like the way he hugged his own child. He remembered when his daughter was this girl's age, young and determined like him, innocent and beautiful like her mother. He sighed as he continued to watch her, not noticing Chief's curious gaze.

John had heard that the captain had a daughter, and that she served in the UNSC as well. Seeing this girl must have reminded him of his own child, and he must miss her dearly. Finally, Keyes turned around and uttered to the doctor,

"When she wakes up, you will report to us, correct?" Owens nodded.

"Affirmative, sir." Keyes gave a slight nod before walking back to the Chief, when Cortana's voice sounded over the intercom.

"Captain, it may take a while for the jump to Atlas." Keyes frowned as Cortana continued, "The jump we made back at Reach fried our slipspace drives, sir. The mechanics are working as fast as they can to get them going." John uttered,

"In other words, we're stuck here." Cortana appeared in a nearby screen and nodded.

"Precisely." Keyes sighed as he pulled out his pipe to place it in his mouth, thinking of what to do next. After a minute, he turned to Cortana.

"Let me know when they're done with the drivers. When they are, stand by for my order for a slipspace jump." Cortana nodded.

"Aye aye, Captain." With that, she disappeared and the screen returned to its normal state, with texts and charts shifting. Keyes turned to John.

"Chief, you're dismissed for today." John froze at that and behind his visor his eyebrows rose as Keyes turned and began to walk toward the exit. "You can always ask Cortana for the map of the Autumn. Feel free to roam around." John stood in his spot, and he saluted.

"Yes, Captain. Thank you very much, sir," he said, loud enough for the captain to hear. Keyes only nodded before the door hissed and closed, blocking the captain from John's view. John lowered his arm slowly, staring at the door in silence. Beeping suddenly sounded behind him and he turned to find Owens connecting cords to the young girl. Owens, noticing him watching, said,

"It's alright, sir. It's only her vitals I need to watch in case something happens." John nodded in understanding before looking to the screen, where green lines were spiking in sync with the beeping. At least she's stable... he thought. He walked back to the wall and leaned against it, watching the girl as Owens checked the cords and monitors. Owens looked up to the SPARTAN questioningly before quickly looking back down to the girl. John saw her glance and said,

"I can leave if you want, Doctor." Owens was baffled at this and she straightened, shaking her hands back in forth in disagreement.

"O-oh no, it's not that I dislike your presence, Master Chief." She looked down at the girl. "I was just thinking that you must care a lot about this child." John raised an eyebrow, waiting for Owens to elaborate. "I mean, do you know her?" John briefly shook his head and Owens blinked. "Then, if I may, why are you here?" John blinked as well. That's right...why are you here, John? He looked to the sleeping girl. You don't know this kid, so why even bother? He mentally shook his head before replying with,

"Just because I'm a SPARTAN, doesn't mean I can't care about the well being of others, Doctor." Owens was taken aback by this and she looked down, making John feel guilty about his retort.

"I wasn't implying that you..." She trailed off and John sighed as he looked down.

"I apologize. What I said was uncalled for..." Owens smiled, and any trace of hurt was fully wiped away.

"It's quite alright, Master Chief. I understand." She returned her focus to the unknown child before her and pulled out a note pad and pen. She glanced at the vitals screen before nodding and writing something down on her paper. "I'm happy that our guest has at least one visitor," she uttered with a smile as she continued her writing. John merely nodded as he watched Owens and the comatose girl. Owens finished writing and lowered her notepad and pen. "Alright. She's perfectly healthy."

"Good to hear," John said. The doctor turned to him and grinned.

"Yes. I'm very glad that she's alright." She blinked and looked to the girl with concerned eyes. "But that scar...I wonder what happened." The SPARTAN followed her gaze.

"So do I..." A silence fell upon them and John turned to the doctor. "Will you look into it?" Owens nodded before meeting his gaze.

"Of course." She turned and began to walk to the doorway, which opened once she approached. She glanced to John with a curious gaze, and John knew what she was wondering.

"I'll stay here for a few minutes, if that's alright." Owens merely nodded with a warm smile and left the room, with the door closing behind her. John stood against the wall in silence, staring at the door for a few minutes. Finally, he sighed and looked to the other occupant in the room. Just where in the hell did she come from? He shook his head, walked to the doorway, and left.

Another Note: Well, any thoughts? Please review. You know I used to dislike Keyes very much, but after reading Cole Protocol, I totally support him now :D I hope I got Chief's character right, he's not very easy, neither is Johnson. As for the pod Emily was found in, it's practically an escape/cryotube pod for one passenger only. Also, title of this series is related to Emily's amnesia and her past. I hope everyone likes this!