Author's Note:
1) Firstly, TWTF people (if you happen to be reading this) - don't get your knickers in a knot, your fic will be updated this weekend. (Yes, it's true.)
2) GAME SPOILERS follow! You have been warned!
3) This has not be beta'd, so I apologize for any errors. Also, if my memory is foggy on any game details let me know and I will fix them right up.
4) Unfortunately I have not been able to trigger the "I Remember Me" side quest, so hopefully that does not effect anything mentioned in these little fics.
5) This "fic" is more like several related oneshots posted as one longer story, like snapshots of events taken at various points throughout the game and then colored with more missing scene stuff and background. Hopefully the flow will not be too horrific!
6) PS: I have taken a tiny liberty with the design of the Normandy and said there are little windows in the com room. There are usually some kind of windows in rooms used for briefings/debriefings, so it seems like there should be some there, even though there isn't in the game. But damnit, I want some there, so now there are windows in the com room. Little ones. Sorry if this causes any of you undue canonical stress. ;)

Part One: Akuze
Kepler Verge Sector, Newton System, Ontarom geosynchronous orbit.

Commander Elizabeth Shepard stood alone in the com room, looking out one of the small observation ports to the planet Ontarom below. She'd had a very brief mission debriefing with Gunnery Chief Williams and Tali, the two who had accompanied her on her latest task, but even after they had left, Elizabeth found herself unable to leave the window.

She just stood there staring down at the planet, trying to come to terms with what she had learned in the facility below its surface. She believed Corporal Toombs had been telling the truth. And she believed the scientist had gotten what he deserved. But something still just didn't seem right. Maybe it was because she had thought for so long she was the only one to make it out of Akuze alive. Then, as soon as she'd discovered that wasn't true, Toombs had gone and shot himself.

Elizabeth had come to terms with Akuze long ago. She had finally learned to deal with the nightmares, the guilt, the anger… but now… now it all seemed so fresh again. Now there were so many more questions that needed to be answered. Before she'd known about Toombs' survival and the real reason behind the thresher maw attacks, the whole incident had been just that – an animal attack. But suddenly Akuze was so much more complicated… so much more sinister…

The door hissed open behind her, but Elizabeth didn't turn. She already knew who it was.

"Are you all right?" Lieutenant Kaiden Alenko asked quietly, stepping into the com room and closing the door behind him.

"Yah, I'm fine," Elizabeth said. It was a reflexive answer, but at the moment the feelings still tumbling around inside her head defied any explanation. From her peripheral vision she saw Kaiden move across the room and stop beside her, following her gaze to the planet still hovering below. The two of them stood that way in silence for awhile. Elizabeth had come to appreciate that about the Lieutenant. He never tried to pry. Never made demands. Just offered an ear when she needed to talk and his opinion when she needed to listen. And silence when she needed to think. He knew perfectly well she wasn't fine at the moment, but said nothing more. He simply stood there next to her, letting her know he was there if she became inclined to share.

His quiet and unassuming nature calmed her, as it always did. She supposed that's why she often sought him out after a mission. And probably what had started the rumors about the true depth of their relationship. Elizabeth never outwardly confirmed or denied such rumors – she never supported gossip aboard any military vessel – but inwardly she had to admit a part of her was drawn to Lieutenant Alenko in a very unprofessional manner. She was sure now he felt the same about her, as well. They had let slip a few flirtatious comments in their past conversations, but were always careful to keep things subtle and under control. There were regulations on that sort of thing, after all. Not to mention how a relationship like that could create an unnecessary distraction from their true goal: to stop Saren at all costs.

But she wasn't too worried about that. Lieutenant Alenko had shown an amazing ability to keep his military duties separate from his personal life. He could switch from fun and friendly to all-business soldier nearly as fast as she could. And that was a very comforting thought. Elizabeth knew she wouldn't have to worry about his feelings for her getting in the way during a battle. He hadn't yet done anything reckless or stupid in an attempt to "protect" her, which is what she had been most afraid of since recognizing their situation for what it was. Every time they stepped off the Normandy, Kaiden was all soldier. Just the way she liked it.

A small smile crept to her lips as another rush of appreciation swept through her. But then it faded as she realized such thoughts of the Lieutenant were doing exactly what she didn't want them to do: distract her. Her frown deepened, her mind going back to the grim and depressing things that had occupied it before Kaiden's arrival. Elizabeth sighed heavily and turned away from the window, pacing to the middle of the room and massaging her temples with her fingertips. She stared at the floor, but still felt Alenko at the window behind her. Still silent and unobtrusive. Still waiting patiently.

"I assume by now you've heard what happened on Ontarom?" she asked suddenly. It wouldn't do any good to keep it to herself, and Kaiden was the one person on the crew she felt most at ease with…

"Only vaguely," came the answer. "Joker mentioned something about writing up a mission report, but I didn't get any specifics." He paused, then said cautiously, "I just heard it had something to do with Akuze."

"That's right," Elizabeth said, her voice strangely toneless. "Akuze."

Another silence followed her admission, and she knew then that Kaiden wasn't even going to attempt to lead this conversation. She turned to face him, crossing her arms across her chest. "How much do you know about what happened on Akuze, Lieutenant?"

Alenko shifted at her question, his dark brown eyes glancing down to the floor. She was making him nervous by putting him on the spot; this was something they had never really talked about before. And Kaiden was a cautious man - he didn't want to offend or make her uncomfortable. "Speak freely, Kaiden," Elizabeth encouraged, understanding his hesitation. Akuze was a delicate subject for many people, least of all her.

The use of his first name brought the Lieutenant's eyes back up to her face. "Yes ma'am." He straightened and gave a nod. "Truth is... I don't really know that much. Just what was broadcast on the general news: your unit ran into a nest of thresher maws... and you were the only one who made it out alive. I thought that was the end of the story, but when I found out we came to Ontarom because of what had happened on Akuze..." He shrugged. "I thought I might come check on you. If that was inappropriate of me –"

Elizabeth waved his words away. "Stop second-guessing yourself, Kaiden. If you piss me off I'll let you know."

The tiniest of smiles pulled at the Lieutenant's mouth. "Yes, ma'am."

"But you're correct," Shepard continued, beginning to pace a line through the middle of the circle of chairs. "There's more to what happened on Akuze than they reported in the news. There's more to it than even I knew, and I was there." She sighed heavily, then stopped pacing and faced Kaiden once more. "You remember why we were sent to Akuze in the first place?"

Kaiden nodded. "Yah, the colony had dropped out of contact… the Systems Alliance wanted someone to go in and check it out."

"Well, we checked it out," Elizabeth said darkly. "Those thresher maws laid waste to the entire colony. There wasn't even anyone left for us to save. And as soon as we hit the surface the threshers came after us… I lost every single one of my men... barely made it back to the landing zone myself…" She trailed off, trying not to get lost in the gruesome memories. "Admiral Hackett sent me a message two days ago," she said, sounding much stronger than she felt and beginning to pace again. "Apparently Akuze had an underground research facility where a few scientists hid out during the attack. They survived."

The Lieutenant frowned. "How come we never knew about them before?"

"I don't think they wanted anyone to know they existed. But eventually someone did find them - Admiral Hackett told me they were being killed off one by one."

"That's all… very suspicious."

"My thoughts exactly. According to the Admiral's information, the last one still living was located somewhere here in the Newton system."

Kaiden lifted one eyebrow. "No wonder we jumped over here so fast. So… what did you find out?"

Elizabeth grunted, shaking her head. "Someone else besides me and those scientists survived Akuze."

"What?"

"Corporal Toombs. One of the men under my command. Turns out he didn't die in the attack. Turns out… the scientists were the ones behind the whole goddamn attack in the first place."

"What?"

"It was all some kind of bizarre, twisted experiment. The scientists were studying the thresher maws… wanted to see what they were really capable of. They provoked the threshers into attacking the colony. The fact that a marine unit showed up in an attempt to help was just a bonus for them. What better way to see how threshers handled weapons fire?" Elizabeth turned her back on Kaiden, feeling her throat tighten at the very thought her men had been sacrificed for such a useless reason. "They recovered Corporal Toombs afterwards." She swallowed hard, feeling tears sting the backs of her eyes. "He said he woke up in a holding cell. That they were thrilled he had survived so they could perform more experiments on him. They wanted to examine the full effects of a thresher attack on human physiology…" She drew in a deep, shuddering breath, unwilling to lose her composure in front of one of her team.

There was a moment of silence, and then Kaiden asked, "Corporal Toombs… was on Ontarom?"

Elizabeth nodded. "He was the one killing the scientists. I don't know when they stopped tormenting him, or if they let him go or he escaped, but he wanted revenge. After what they did to him – after what they did to all of us, to all those colonists – I don't blame him." She clenched her fists at her sides. "I would have killed that son-of-a-bitch scientist myself if I had known earlier."

Shepard waited to see if the Lieutenant would criticize such sentiments – he was the one always warning her about cutting corners, after all – but he seemed to sense this was not the time for such a comment. Instead he said, "Surely you don't think the Systems Alliance planned that attack… do you?"

Elizabeth closed her eyes, shrugging. "I don't know. I never found out who was really behind it all. We got to the facility right as Toombs was confronting the scientist - Dr. Carson, I guess his name was. The Corporal told me what had really happened on Akuze… and of course the good doctor denied everything."

"And you believe Corporal Toombs was telling the truth?"

Shepard spun to face Kaiden, her glare sharper than she had intended. "I trusted every one of the people in my unit with my life," she said in a low voice. "Of course I believe him."

"I'm sorry," Kaiden stammered, "I wasn't trying to – I didn't mean for it to sound that way…"

Elizabeth exhaled loudly, trying to force herself to relax. "I know," she admitted quietly. "It's all right. I didn't mean to snap at you. I'm just… I'm just a little upset…" She sighed again, swallowing hard. "Corporal Toombs shot himself."

Kaiden blinked, obviously finding it just as difficult as she was to absorb everything. "Oh. I'm… I'm sorry…"

"It was because of what they did to him," Elizabeth growled, stalking back to the window, glaring down at the planet. "He wanted to kill those scientists for what they had done, and I agreed with him. I told him to shoot Dr. Carson. It's what he wanted. It's what I wanted. I thought it would help." She glanced at Kaiden from the corner of her eye, attempting to gage his reactions. His brow furrowed, but otherwise he was hard to read. He watched her intently, listening, waiting for her to go on. So she did. "It helped Toombs find some peace, I think. But he was too far gone for me to do anything else but let him have that final moment of vengeance. After Dr. Carson was dead, and Toombs killed himself, I… I don't know."

Shepard moved from the window to one of the chairs and sank down into it, dropping her head into her hands. Talking to someone about the Ontarom mess was therapeutic, and yet she was hesitant to divulge the depth of her uncertainty on the subject. Lieutenant Alenko was a subordinate, no matter what feelings had thus far grown between them. And she was supposed to be his commanding officer. How much of this weakness could she afford to show him?

"Commander," Kaiden spoke up softly, coming to stand beside her, "I know I've only served with you for a short time now, but if there's one thing I've learned since you came aboard the Normandy, it's that you don't stand for the murdering of innocent people. Dr. Carson and the other scientists killed a lot of people. A lot of people who didn't deserve to die. A lot of people who didn't have to die."

Elizabeth nodded mutely, not trusting her voice. The tears she'd managed to restrain before were now blurring her vision; she blinked them back quickly as Kaiden stepped closer.

"You did what you felt was right," the Lieutenant assured her. "And for what it's worth, I think you made the right call. Dr. Carson was willing to sacrifice hundreds of lives just for the sake of studying an animal – who knows what he might have tried next."

Shepard swiped quickly at her tears, then looked up to Kaiden and graced him with a half smile. The fact he'd come to the same conclusions as she had eased the nagging doubt that had assailed her since leaving the Ontarom compound. Though she knew a part of her would always blame herself for Toombs' death, the weight of her decision regarding Dr. Carson seemed lessened. It wasn't that she necessarily regretted his murder – the man deserved worse than a bullet in the brain as far as she was concerned – but she couldn't help but wonder if she should have arrested him instead. Maybe then she could have gotten some answers… maybe it would have been better for Corporal Toombs to have less blood on his hands and more time to cope with what had happened to him.

In the end she had decided it was simply too risky to arrest the doctor. The man had to pay for his crimes… for Toombs' sake, for her sake, for the sake of the fifty marines who had died at Akuze. She couldn't take the chance of politics getting in the way of Dr. Carson's trial. She had been right in not wanting to take that risk. And Kaiden was right - the man was dangerous. Now he couldn't hurt anyone else ever again.

"Thank you, Lieutenant," she whispered. "I needed that."

He gave her a small smile in return. "I know."

Their eyes met and held, and Elizabeth's breath caught in her throat. They way he looked at her… it made her skin tingle. She opened her mouth to say something, but words failed her. She coughed to cover her speechlessness, then stood from the chair. "Well…" she finally managed, "I should probably go make the report to Admiral Hackett…"

Kaiden snapped out of his stare. "Oh, right. Of course."

Shepard gave him a full smile this time. "Thanks again for the talk, Kaiden."

"Anytime, Commander," he returned.

Elizabeth moved for the door, looking back once over her shoulder as she activated the controls to exit. The Lieutenant was still watching her, but when he saw her look back he hastily moved toward one of the windows. Shepard tried hard to suppress the grin itching at her lips, stepping through the doorway and continuing on toward her quarters. She had the distinct impression that her relationship with Kaiden Alenko had just taken another step in a forbidden direction.

For some reason that knowledge didn't bother her as much as it should have.