Author's Note: This is another stand alone from the same story line as The Reason. It is the first time we're seeing something from my Shepard's point of view. I don't have too much else to say about it. It's not necessary to read The Reason to understand this, though, you could if you wanted to. :) I would love to hear what you think. Enjoy. - TLC

Then, She Woke Up

The last forty-eight hours had been some of the most baffling hours of her life. She was thankful for the gentle lighting, and general silence of the Captain's Cabin – her new quarters. Currently, Sloan Shepard was sitting at the desk in the office area of her cabin. There was a large fish tank stocked with exotic fish to her left. There was a glass case in front of her desk filled with model ships: Alliance, Geth, Quarian, Turian, there was even a model of Sovereign. She still wasn't sure what exactly was going on. She looked down at her hands, they looked the same but better. Her nails were neatly trimmed and though not polished, they shined. There were no hangnails or torn cuticles. Her hands were warm. They hadn't been warm, for … as long as she could remember.

As long as she could remember…

Two years. They told her two years had gone by while she slept. Slept… was rebuilt. Rebuilt… what did that even mean? She sighed and dropped her head into her hands, scrubbing them roughly over her face. She closed her eyes, leaning back in her seat. The last thing she remembered was the Normandy being attacked. Ordering everyone to the shuttles. Bodily shoving Joker into his pod before being spaced. She remembered floating over Alchera and the soft hiss of the leak in her suit. She remembered feeling the cold seeping into her bones as her lungs burned for oxygen.

Her last thought had been of Kaidan. The way his eyes would light up when he smiled. The feel of his calloused hands on her bare skin. The way he held her by nearly folding himself around her like she was this precious, delicate thing he got to hold. The brush of his stubble against her neck. She bit back a sob as she remembered everything about him, like it had been just yesterday she had held him. For her, it had been. For him, apparently, it had been years. She had no way of getting in contact with him, though she wanted nothing more. She pulled her legs up so her feet were on the seat in front of her and wrapped her arms around them. The long, dark hair fell with a familiar weight down her back.

She had never been more confused in her twenty-nine – thirty-one? – years. She'd lost consciousness floating over the Normandy after it had been attacked. She woke up two days ago on a Cerberus space station. Cerberus. She shuddered unable to comprehend that she was working for… not for, never for, but with the terrorist group. With the old Normandy, she'd taken out more than one of their cells. Now, she was surrounded by unfamiliar people; people she didn't think she'd ever be able to trust at her back. Thankfully, there were two exceptions: Joker and Dr. Chakwas.

The relief she had felt when she saw her pilot was immeasurable. He'd seemed surprised, and had chuckled, when she'd thrown her arms around him and held him close. She had just needed to latch on to something, anything to make it all feel real. She pulled back and looked at his face, blushing slightly. He looked good, but different, in Cerberus white, black, and yellow. She preferred him in the Alliance's greys and blues. As they walked down a hallway, he explained that after the Normandy had gone down, the Alliance had grounded him. Cerberus had offered him a position, and gave him a ship to fly. It was then she noticed he was walking without crutches. He'd blushed and rubbed the back of his neck with an embarrassed smile. "Another benefit of the private sector?" He suggested and she shook her head. "That's not all… take a look at this…" He gestured with his chin towards a window. When they looked out, the lights at the dock turned on and illuminated a reincarnated ship, reminiscent of the Normandy but much larger. Shepard suggested they name her and looked up catching Joker's eyes. They grinned together. There really was just one name for a ship that beautiful: Normandy SR-2.

She had gone to the med bay almost as soon as she'd stepped on the ship. Joker had told her that Dr. Chakwas was there but she needed confirmation. Sure enough, the Doctor was aboard, in her Cerberus uniform. Her green eyes filled with tears when they met Shepard's. Chakwas wrapped her arms around her and held her close. Shepard took a deep breath burying her face in Chakwas's neck. The doctor forever smelled like cinnamon and medi-gel. "What the hell is going on?" Shepard whispered.

"That's quite the question," Chakwas answered. "I have access to the files from your time with Cerberus. I've read through them," Chakwas admitted as she led Shepard towards one of the cots in the bay. "It's not easy reading, but if you want to see them, I can forward them to you," Chakwas offered and Shepard blanched as she sat on the cot.

"Just… tell me what I need to know?" Shepard asked quietly, her voice sounded odd to herself; young and with an innocence long since lost. Chakwas spoke and Shepard only understood some of it. The Project… Project Lazarus had been headed by Miranda Lawson; the beautiful, buxom, brunette scientist who answered directly to the Illusive Man, the man behind Cerberus. She had been there when Shepard woke, and had helped her, and the ex-Alliance head of security Jacob Taylor, escape the station while it was under attack. Project Lazarus involved attaching cybernetic implants to her skeletal system to recreate her bones, reconstruction of the skin, and fluids to restart blood flow and internal organs. She ran her hands over her thighs as she looked to her body. How much of her was her and how much was machine? She swallowed hard.

They had also upgraded her biotic implant. She went from an L3 to L5n implant. She wasn't even sure what that meant, though, she noticed at Freedom's Progress that her biotics were stronger and could run longer without overheating. It would take some time to get used to. "Wait… they regrew my skin?" She asked and Chakwas nodded. Shepard licked her lips and her hands went to her face. She hadn't seen herself since she woke. She felt for the scar that cut across her face and when she felt nothing0 but smooth skin, her eyes filled with tears.

"They're all gone," Chakwas had whispered and Shepard ran both hands back through her chocolate hair. "But there are new scars. Scars from your … reconstruction that didn't have time to heal. You were woken earlier than planned," Chakwas explained and Shepard's following laugh was missing the humor.

"So, I wasn't done baking?" She asked grimly and Chakwas frowned. She started talking about how a positive attitude and actions may help the healing process and Shepard stopped listening. It all seemed so … science fiction. Which was really saying something considering she was currently on a space ship hurtling through the galaxy at warp speeds. She hadn't looked at her scars, yet. She didn't know if she wanted to.

Shepard stood from her desk and took the three steps down to the living area of her quarters. There was a couch to her right, which stretched along two walls and met in the corner with a coffee table in front of it. There was a closet to her right and a bed in front of her. There was also a private use station to the right of the bed. She went to the closet and sifted through the clothes. Every piece had the Cerberus logo. She swallowed audibly. The next time they stopped at a station she would be purchasing some civilian clothes. She turned and moved to the couch. She sat and lifted her feet to rest on the table, crossed at the ankle.

She looked up and found a skylight above her bed. She could see the waves of energy racing over the ship as they traveled at warp speeds, and the stars moving beyond that. She swallowed hard and closed her eyes. Cerberus had brought her back because the human colonies were under attack, and neither the Alliance nor the Council were taking it seriously. Apparently, some things don't change. Attacks on human colonies were never seen as a priority. The colony of Freedom's Progress was most recently attacked, and before Joker had shown her the Normandy SR-2, Miranda, Jacob, and she had gone to investigate the colony.

It was the most bizarre experience. She'd seen colonies after they had been attacked by slavers, and by geth, but this was different. It was like the fabled Rapture. All of a sudden, everyone was gone. Regardless of what they were doing at that instant. There were tables set for dinner, beds messed, and vid screens left on. The oven was on in one home, the meal inside charred and smoking. There were no signs of struggle. It was like everyone had vanished.

Then the mechs had attacked, and Miranda had commented in her thick Australian accent, that the security systems at the other colonies had been disabled. She hypothesized that this meant they weren't alone here. After the mechs had been dispatched, they opened one of the pre-fab homes and found a group of Quarians. The startled aliens instantly drew their weapons.

One Quarian stepped forward, "Shepard?" Tali's familiar trill rang out in the small area, and Shepard felt the warm rush of familiarity and instantly dropper her weapon signaling for Jacob and Miranda to do the same. Surprisingly, they had followed her order. "You're alive?"

"Appears so," Shepard responded. "Cerberus brought me back to find out why human colonies are being attacked," She answered and Tali was able to get the rest of her group to lower their weapons as well. Shepard was suddenly proud of the young woman. She had obviously matured during the last two years, and was clearly the leader of this group. She seemed well.

Tali had brought her team here to find Veetor, one of her people who had been at the colony for his pilgrimage. It became apparent, then, that it must have been Veetor who reprogrammed the mechs to attack anything that moved. Tali ordered her team to work with Shepard in order to find him. They split into two groups, and before long they did. He was sitting in the security office watching the vid screens. He was traumatized, and after a moment, Shepard had lifted her omni-tool and powered down the screens to bring his attention to Tali.

He explained that the colony had been attacked, and was speaking in circles. He pulled up the feed from the attack and froze it on one frame. "The Collectors?" Miranda asked and Shepard felt a trace of fear slide down her spine. The Collectors are a race of alien that few have seen. They live beyond the Omega 4 relay, which no ship has ever returned from. Well, now that had a name for their enemy. Shepard had turned to Tali and asked her to come with. She knew there was no way she could turn away while the colonies were being attacked. She was terrified of going on this mission without someone she knew at her back.

The regret was plain even in her trill when Tali said she wouldn't be able to come with her. She had to get Veetor back to the Fleet. This was when Miranda spoke up and insisted on bringing Veetor with them. Tali had reacted instantly, and Shepard was grinning inwardly. Tali was protecting her people as viciously as Shepard would have. Shepard raised her hand, "Tali, can we have a copy of his data?" She asked her friend and Tali had sighed. Shepard could feel the anger coming from the Cerberus agent behind her, but she didn't care. This was the first test. Would they honor her order and follow her command?

Tali agreed and Miranda stepped down, though, she hated to do it. They went their separate ways, Tali with her team back to the fleet and Shepard with Miranda and Jacob back to their shuttle. When they returned to the shuttle, Shepard had another meeting with the Illusive Man. Granted, she hadn't actually met the man, and they were conversing through a long distance communicator Shepard didn't fully understand. She agreed to work with Cerberus to stop the Collectors, but then she was done. She tried to insist on gathering her own crew and that was when she'd learned they were unreachable. Garrus had fallen off the grid. Wrex was on Tuchanka with his people. Liara was working on Illium. Clearly, Tali had her own work to do. She'd asked about Kaidan, and didn't miss the hesitation in the Illusive Man's eyes before he answered. "He's still with the Alliance. Commander Alenko's file is surprisingly well-classified," Shepard had sighed in resignation.

She would have to take his word then, though she hated to do it. She agreed to gather the crew he had assembled for her. Commander Alenko. He'd been promoted. She smiled sadly. He deserved it, and she hoped he was doing well. She closed her eyes again, and she could hear him. The way he would whisper in her ear as she dozed off. She sighed when she felt the tears in her eyes again. It had been two years. He had most likely moved on. There was no point in dwelling.

She was startled when she heard the alert from her personal terminal. She stood and went to the desktop and sat down before she logged on. She pulled her hair back and twisted it off her neck. It was a message from Anderson. Her heart swelled with anxiety and loneliness as she read over the message. She could almost hear the sadness in his voice as she read the message asking her to come to the Citadel and meet with him. "EDI?" She called out, still not entirely comfortable with the AI on board.

"Yes, Commander," The slightly digital, yet soothing voice rang out in her room as the blue orb lit up in the corner.

"Shepard, please, EDI," She asked and the AI responded in the affirmative. Shepard was hardly a Commander at this point. "Have Joker set an immediate course for the Citadel," She ordered.

"Yes, Shepard," The AI answered before blinking out. Shepard turned and looked around the room. She was suddenly curious as to how many listening or video surveillance bugs were hidden in her quarters and she wished she'd had Kaidan teach her to scan for them. She sighed and scrubbed her hands over her face feeling suddenly very fatigued.

As her hands moved over her smooth skin, she felt the anxiety race through her again. She never considered herself a vain woman. The only reason she wore the make up she did was to make some of her scars seem less noticeable. She wanted to appear approachable to her crew and she always felt the scars made her more intimidating. The scars from Mindoir, however, simply meant a lot to her. Reminders of her ability to survive. Reminders of her family. They had become a strange part of her, of who she was.

She walked to the bathroom and the door sighed open before her. There was a large private shower, toilet, and sink in the room. She turned and looked to the sink. Slowly, she lifted her bright blue eyes to the mirror. She immediately looked for the scar that cut across her face. It was gone. Smooth, alabaster skin replaced the once angry red line. Even the missing hair from her eyebrow had been replaced. Instantly, tears filled her eyes. She stepped closer and looked for the dotted scars from Akuze. Gone. She pulled off her shirt, and stood topless in front of the mirror. The scar on her shoulder, from Feros, that Kaidan mended was gone. She turned. The burn scar across her back, beneath her breast, the puckered scars on her belly. All gone. She pulled her pants off. Her favorite scar, the one that Kaidan used to love to trace, on her thigh, was gone. A sob escaped the back of her throat as the tears spilled from her eyes. She turned the shower on and finished stripping.

She stepped into the shower and let the hot water wash over her unfamiliar body. She wondered, as she cried, what Cerberus had put inside her? Mind control chips? Tracking devices? A kill switch? How much control did she really have over her own body? She could feel her biotics reacting to the maelstrom of emotions raging through her, and felt the empty ache as she wished Kaidan were here. There was always something comforting about his presence; even before they became lovers. Her biotics always seemed to rage near the surface, and her fuse was short. When he was around, it was like her biotics took their cues from him, and when she was near breaking if she caught his eyes it was like a cool wave breaking over her and calming her down.

Then, he kissed her in the elevator and everything was suddenly different, better. He promised he would always stay with her before he'd spent the night with her before Ilos. They had always been able to find a rhythm while groundside on a mission. After their night together, it was almost instinctual. She had never felt so connected to another person. Then, they shared those amazing weeks in Vancouver. Never in her life had she felt so adored, so cared for, so precious. The effect he had on her was intense to say the least. It was no wonder she had fallen for him the way she had; so fast, so hard, so deep.

Why hadn't she ever told him?

She washed quickly, absently taking note of the angry red scars in her new skin that seemed to glow from the presence of cybernetics beneath the skin. She stepped out of the shower, suddenly exhausted, and dried quickly as she walked to the bed. She turned off the lights, and crawled under the blanket, still naked and damp. She closed her eyes and let herself fall asleep.

There was no pain. There was no fear. There was no doubt. She wasn't Sloan Shepard, but she was. She was comfortable, warm, and happy. She was alone, but not. She knew her family was with her. She could feel them nearby. Her mother. Her father. Her brother.

Slowly, they grew more distant, and she realized she was missing something. Someone.

Doubt returned. Where was he?

Fear returned. Had he left her?

Pain returned. Her eyes opened and the bright lights assaulted her, and every part of her body ached from a lack of use. She whimpered, "Kaidan?"

The lovely, Australian voice rang orders out over her head pulling her from her thoughts. She followed blindly.

She turned and found herself back on the Normandy, in her hardsuit just having ejected Joker from the ship. The beam from the ship cut through the Normandy and sent her off, floating through space.

She heard the hiss.

Felt the ice in her bones.

Felt the fire in her lungs.

She thought of Kaidan's smile.

She opened her eyes, and saw the stars twinkling in the vast expanse of tarlike space around her. She was gasping for air as she sat up in bed. Her heart was racing and her naked body was covered in sweat as she struggled for air and fought the tangle of blankets twisted around her.

She fell from the bed and it wasn't until she hit the floor that she was able to catch her breath. She sat still for a long while, letting herself calm down. She supposed waking up beneath the starry night sky wasn't such a great idea for someone who had nearly died in space. She got off the floor, and dressed in a long T. She grabbed her blanket and a pillow and curled back up on the couch. It wasn't quite morning, yet, but sleep proved elusive the rest of the evening.