A/N: Alright, this chapter is almost strictly Daniel and John, though a few others make some brief appearances. It's a little angsty, but it should start to answer a few questions. This is a longer chapter. :) Enjoy!

Chapter 2 - We're Brothers

John was sitting on the floor near the far corner of the room, knees drawn up to his chest and staring at the opposite wall, when Daniel walked in. He met the archaeologist's eyes for what seemed like an eternity, but was really only a second, before returning his gaze to the wall, and hunching in on himself more.

Daniel recognized the guarded position. It reminded him of the John he'd met all those years ago, especially with the way John's eyes had screamed at him. Taking a deep breath, he slowly made his way over and sat down next to John, matching his posture.

Neither man spoke for a few minutes.

Realizing the situation they had found themselves in, Daniel swallowed guiltily. He hadn't seen or talked to John since the mess with the Replicators and the expedition's return to Atlantis. Jack had been the one to fill him in on everything, and reassure him that Landry was not getting his way, and John wasn't going to be court-martialed, again — Jack had told Daniel it'd be kind of hypocritical of him to punish John for doing the same thing he'd have done if he'd been in John's position. Looking at John now, Daniel wished he'd actually sent the email he kept meaning to write, but he'd kept getting distracted — or kidnapped — by the Ori.

"Ya know," Daniel finally started quietly. "I tried to find you. Later. But they never told me your real name." The way John stilled imperceptibly told Daniel he had his attention. The corner of his mouth turned up sadly. "When I got back that day and you were gone… They told me they'd found out who you really were; that you'd run away, but they'd found your family, and Mrs. Jenkins had taken you home."

"No she didn't."

Daniel glanced over at John, but John wasn't looking at him. He was staring at his hands.

"The cops took me back. Not Mrs. Jenkins." He sighed heavily, and finally turned his head toward Daniel. "I wanted to stay." The gut wrenching admission was followed by a humorless chuckle, and he leaned his head back against the wall. "But even if I couldn't, I didn't wanna go back." John shrugged, but didn't say anything else.

He didn't have to. Daniel filled in the blanks. He could hear it in John's voice. Watching him for a minute, Daniel smirked, and asked lightly, "You know what my first thought was after we met again in Antarctica and I realized who you were?"

John didn't reply, but his eyebrows raised fractionally.

"I thought 'Huh. His name really is John.'"

He didn't laugh, but the wide smirk that lit up John's face said it all. "I did tell you…"

Daniel chuckled. "Yes. Yes, you did."

Turning somber once more, John had ducked his head as he muttered, "I'm sorry. For dragging you into all this."

Grabbing John's arm, Daniel waited until John met his eyes, however reluctantly, before he spoke firmly. "John, listen to me… This is not your fault. And we're gonna get your memory back."

John opened his mouth, but Daniel cut him off with a look.

"I would've been here whether you'd said anything or not." Seeing John's furrowed brows, Daniel explained, "Jack — General O'Neill — put me as your next of kin for exactly this type of situation. So I'd know if something happened to you. Just like he'd make sure you knew if anything happened to me."

It was a minute before John replied. But he hadn't looked away from Daniel. The archaeologist saw the moment his facade crumbled. "Danny… The last thing I remember clearly is being at Stanford. And obviously I'm not in college anymore." He'd tried to play it off as self-deprecating, but Daniel heard the fear behind the helpless way John had said his name.

Remaining calm and steady, Daniel nodded slowly. "Ok… That's a start. It means you know who you are, and you remember at least half of your life. Some people who wake up with amnesia can't even remember their name, or anything about themselves." He was still holding onto John's arm, and could feel his reassurance working as the younger man's taut muscles began to relax fractionally. "You said 'clearly'. Do you remember anything else?"

The archaeologist wasn't pushing, and his supportive presence was having a calming effect on John. The way he spoke said volumes about how grateful he was to have someone on his side. "Just flashes. Bits and pieces that don't make any sense." He shook his head, and used the hand on his free arm to rub his forehead as he closed his eyes and scrunched up his face.

"Hey." Daniel gave the arm in his grip a small shake. When John hesitantly met his eyes, Daniel smiled. "That means it's coming back. It's just gonna take time."

John held his gaze for a long moment, his eyes searching. Satisfied with what he saw in the other man's eyes, he gave a jerky nod.

Giving a nod of his own, Daniel released his hold and made his way to his feet. Looking down at John, he offered a hand. "Come on. Let's see if we can't jog some more memories."

Furrowing his brows, John accepted the hand, asking, "How?" as he stood.

"I know you don't keep a lot of personal items, but you have lived in this city for most of the past three years." Daniel shrugged. "Sometimes just being in familiar places can help you remember." Frowning when he saw John look down and shuffle his feet, Daniel asked, "What's wrong?"

Rubbing the back of his neck, John glanced up at him and shrugged. "I don't think I'm allowed to go anywhere."

Daniel rolled his eyes, setting his jaw as he held back verbalizing the thoughts that were apparently written on his face, as John raised his eyebrows. "I don't care. Come on."

This time, John didn't argue.

When they exited the isolation room, the guards that had wisely not tried to prevent Daniel's entrance were gone. Though Daniel caught the flash of confusion when John narrowed his eyes at their absence, neither man commented, and John just followed Daniel's lead.

They didn't run into anyone else until they reached the second corridor. At first, John tensed, but he forced himself to loosen his stance when Daniel practically sagged in relief upon recognizing the man.

"Hey guys." Cam's smile and easy drawl had a relaxing effect on John as well.

Giving him a nod, Daniel glanced at John. "This is Lieutenant Colonel Mitchell. Cam and I work together. He offered to come with since, other than me, he's the only one in the program who knew you before you got read in in Antarctica."

Grinning, Cam held out his hand. "We met all the way back in flight school."

John shook the offered hand, nodding slowly. Narrowing his eyes, John tilted his head. "Shaft."

Cam chuckled. "That's right." Shooting Daniel a smirk, he told his teammate, "See."

Daniel barely managed not to roll his eyes at his team leader. Instead, he asked a question. "So, what's up?"

"General O'Neill was still in the conference room last I checked. But I did run into Major Lorne, and he said to let you guys know that if you need anything, just ask." Turning to John, Cam smirked. "He also asked me to tell Sheppard he'll take care of everything until you're back on duty, but that, while he doesn't mind helping with your paperwork, he does not want your job so 'please hurry back'." His amusement was almost tangible.

John chuckled. "I like him."

Smiling, Daniel nodded. "Lorne's a good guy. In one of your emails, you told me to thank Jack for recommending him."

"Jack?" John's brows were furrowed.

"General O'Neill."

"Ah…" Nodding slowly, John's eyes darted between the other two men. "So… You guys are supposed to help me remember everything?"

"That's mostly Jackson's thing." Cam shrugged and grinned. "I'm just a friendly face. And moral support."

Raising his eyebrows, John's mouth was twitching in amusement while Daniel rolled his eyes.

"Yes, thank you Colonel Helpful."

Cam smirked at his teammate. "Anytime." Looking at his watch, he added, "Well, I better get going. Lorne said Ronon is training some of the marines in about ten minutes, and I wanted to watch." Turning serious, he met both of their eyes. "Let me know if you need anything."

The corner of John's mouth quirked upward.

Daniel gave a small sigh. "Thanks Mitchell." His appreciation did not go unnoticed.

Cam grinned and slapped him on the shoulder in return before nodding at John. "See ya around Sheppard."

John waved as he and Daniel watched the colonel continue on around the corner. Once he was out of sight, he smirked at Daniel. "He's like a big puppy, isn't he?"

Daniel dropped his head into his hand. "Oh god yes."

John chuckled at the dramatics.

Looking back up and shaking his head, Daniel said, "Come on. Transporter is just down the hall."

By the time they reached John's quarters, Daniel could see the questions piling up in John's brain etched into the younger man's expression.

John's face was scrunched up as he looked around the room, picking up odds and ends he narrowed his eyes at.

"Anything?" Daniel asked lightly. He wasn't pushing, and he knew John didn't take it as such.

"It…feels familiar, but —" John shook his head, rubbing his forehead.

Daniel knew he was trying to remember, but was getting increasingly frustrated because he couldn't quite get there — like a word on the tip of your tongue but you just can't think of it. So, Daniel had them sit down, and he explained the Stargate Program, Atlantis, and how John had gotten involved — how they'd met up again after all those years.

"So…I've got some mutant gene?" John's skepticism was clear, but Daniel kept his patience.

"It's not mutant…sort of. Look, it basically just means you can use the Ancients' technology. In fact, you seem to have a natural aptitude for it. It comes easy to you. And your gene is stronger than anyone's, even Jack's — who had the strongest we knew about until you."

Daniel's words had a calming effect on the anxiety he'd noticed beginning to rise in John.

"Look, just try it," Daniel suggested. Glancing around, his eyes landed on the door, and he looked back at John and said, "Ok, just think about opening the door."

"What?" John asked shortly, but at the same time, the door swooshed open, revealing a general with an airy expression that might've been classified as surprised on anyone else.

"Was that me or you?" was all Jack said as he entered the room.

"Me. Apparently," John muttered, looking back at Daniel who smiled.

"See. Told you."

"How is that not mutant?" John retorted.

Daniel rolled his eyes, but Jack smirked. "Whatever it is, it's cool," the general shrugged.

John looked back at the older man, his brows furrowing as if he was trying to figure out how he knew him.

Seeing this, Daniel introduced his friend. "This is Jack — General O'Neill."

"I'd say 'nice to meet you', but I'm guessing we've already met," John said to the general, managing to look both apologetic and frustrated at the same time.

Jack waved him off. "Don't worry about it. When Daniel got amnesia, he showed up on some random planet stark naked. Didn't even know his name or where he was from."

"Jack!" Daniel was glaring at him, studiously ignoring John's raised eyebrows and curious expression.

"Do I know this story?" he asked with a smirk.

Daniel huffed out a long breath, dropping his head.

Jack grinned, and told John, "I'll tell ya later."

Shaking his head, Daniel ignored their amusement and looked up at the general. "Was there something you needed Jack?" he asked pointedly, trying to change the topic away from his own embarrassing moments.

Shooting a smirk at his friend, Jack nodded and turned serious when he looked back at John and pulled out a flash drive. "Thought you might wanna take a look at this."

John took the drive slowly, giving it a cautious look, before sending the older man a questioning glance. "What is it?"

"That is your entire military record," Jack answered frankly. "From the time you signed up until now. Unredacted."

John raised his eyebrows at the last bit of information, but Jack didn't elaborate further.

Shrugging, the general added, "I know not everything makes it into reports, but I figured it might help jog some memories."

Swallowing, John's eyes turned back to the flash drive. He appeared even more wary of it now, and the other two didn't miss the way he hunched in on himself more. "Thanks," he mumbled.

Sharing a look with Daniel, Jack cleared his throat. His voice and tone were gentle and reassuring when he said, "You guys let me know if you need anything."

John nodded slowly, but didn't look up.

Daniel gave his friend a grateful look, and replied sincerely, "Thanks Jack."

Nodding, the general shared one more look with the archaeologist before leaving.

The room was silent for a couple minutes, before John finally broke it, in a voice that was so quiet Daniel almost didn't hear.

"Do I wanna know what's on here?"

Sighing, Daniel's face scrunched up in consternation. But he answered honestly. "Probably not everything." He saw John nodding to himself, and said firmly, "But that's a large portion of your life. It's part of who you are. Whether you want to know or not…You need to know."

When John met his eyes, Daniel was immediately reminded of right after they'd first met, and Diana had tried getting John to open up and tell them what had happened, where he was from. It was fear. Fear of the truth.

John looked away quickly — seemingly realizing what Daniel had seen. "Do you mind if — You know?"

Daniel did know. He nodded. "Sure." Watching John for another moment, he sighed and stood up. "I'll get us something to eat while you take a look at that."

"I'm not really hungry," John tried to argue.

"Oh, it wasn't a question," Daniel shot back easily.

So, after he made sure John could get on the computer and access the files, Daniel headed to the mess hall to get them some food.

He was halfway there when someone stopped him.

"Dr. Jackson."

Daniel held in his sigh as he turned to greet the woman. "Dr. Heightmeyer."

The smile she gave him told him she knew his was fake. "I was hoping we could talk for a few minutes."

"About what?" he asked innocently, but again she gave him a knowing smile.

"About Colonel Sheppard," she answered anyway. "I apologize for not being in the meeting when you arrived. I had a prior appointment, and at the time, the assumption was that Colonel Sheppard was not really Colonel Sheppard, so my services were only minimally required. However, now —"

"Now that you know he was telling the truth, you want to help figure out what's going on and help him get his memories back," Daniel finished for her.

The psychologist nodded. "That's correct."

Daniel sighed, rubbing his forehead. "Doctor, you've known John for three years." He looked her in the eye when he asked, "Do you really think he's gonna talk to you, especially in this situation?"

This time, her smile was amused as well as knowing. "That's where I was hoping you could help me, Dr. Jackson." When Daniel raised his eyebrows, Kate elaborated, "John remembers you. He trusts you. And with your relationship, you're the one who knows the most about him."

Letting out a long breath, Daniel closed his eyes for a second before returning his gaze to the doctor. "Kate — can I call you Kate?"

"Of course," she encouraged.

"Kate," Daniel sighed. "Until Jack dragged him down into the Antarctic base three years ago, I hadn't seen or heard from John in over twenty years."

There was that knowing smile again, but now it held sympathy as well. "Daniel — can I call you Daniel?"

Daniel couldn't help but smirk at the way she was repeating his words, but nodded in reply.

"Daniel, I have read both yours and John's backgrounds." Kate gave him a steady look as she informed him, "I know what you both went through. Though, I will admit that until you showed up and confirmed John was your brother, I didn't make the connection between you."

"And now that you have?" Daniel prompted, knowing she was going somewhere with this, but not quite sure he wanted to know where.

Kate sighed heavily. "You're right. I don't think John will talk to me. In fact, I think — like the treatment he experienced before you arrived — that it might do more harm than good in this situation." Daniel nodded his agreement before Kate added, "But… I do think he will talk to you."

Taking a deep breath, Daniel rubbed his forehead again. "And you want me to keep you updated?" he guessed with a sigh.

The smile she gave him now was gentle. "I would appreciate it, yes," she agreed, but then assured him, "But I don't expect you to divulge details. I'd just like to know that he's doing okay." When the archeologist gave her a calculating look, she smirked. "I can work on getting details after his memory has returned and he's back on duty."

Daniel couldn't help it. He chuckled. "Yeah. You fit right in here."

Kate smiled. "I'll take that as a compliment."

"It is," Daniel agreed. "John said you're good. And that means a lot."

There was that knowing smile again. "Yes, it does."

0

John had barely touched the food Daniel brought back for him. His attention had been solely focused on the files he was reading.

Daniel didn't try talking. Despite Kate's belief that John would talk to him — a belief he couldn't really refute — Daniel knew John needed time to process. John wouldn't talk unless he wanted to talk, and trying to force him to do so would only prolong his silence. Daniel had watched it happen when they were kids, and while John seemed to have picked up the habit of talking circles around people without ever actually saying anything of value, he still valued the silence. Besides, right now, he wasn't the current John Sheppard. Right now, he was trying to piece together half his life.

When John finally closed the laptop, he took a deep breath and dropped his head into his hands as he leaned on the desk.

Daniel waited patiently until John turned to look at him. He barely managed to maintain a neutral expression when he saw the turmoil in the younger man's eyes; eyes that were begging him to make sense of it all, something the archaeologist couldn't do for him, no matter how much he wished he could. He remembered how hard it had been for him when he had returned to human form after his ascension, and how hard it had been to not have all of his memories.

"There any booze in this city?" John's tone was light, but his voice still cracked.

Not commenting on John's — poor — attempt to hide his distress, Daniel simply nodded toward the mini fridge.

John opened it, and found the beer. He shrugged one shoulder, muttering, "It'll do." Pulling one out, he glanced back and held it up in question.

Daniel nodded, and John handed him the beer before pulling out another for himself.

They sat there for a few minutes in silence once again, each just sipping their beers — or practically chugging, in John's case.

Once his can was empty, John sighed heavily, staring hard at the can as he traced the lettering with his fingers.

Daniel watched him closely, knowing he wanted to ask something. When John finally looked up, Daniel had a feeling he knew what the question would be. And he was right.

"Why are you here?" He tried to play it off as nonchalant, but the archaeologist knew him too well.

"You know why." Daniel's voice was quiet, but firm.

John wasn't easily deterred though. "We barely know each other. Hell, until a few years ago, we hadn't even seen each other for over twenty years. You don't —" He paused and looked away. When he turned back, he kept his eyes down and focused on the empty beer can. "You don't know." He didn't elaborate further, but he didn't have to.

"I don't need to," Daniel told him firmly. When John looked up and opened his mouth to argue, Daniel cut him off sharply. "No, I don't know everything you've been through, or what you've done. But I know enough. And I know you." John still looked like he wanted to argue, but Daniel's expression kept him from doing so. "Regardless of how long it's been, or how much we both suck at the whole communication thing… We're brothers." When John averted his eyes, Daniel sighed heavily, taking off his glasses and rubbing his forehead with the back of his hand. "John… Look… I know I'm terrible at this stuff, but I meant what I said back then. And I mean it now." Waiting until John met his eyes, Daniel said emphatically, "We're brothers. Nothing changes that."

The younger man's attention was back on the empty beer can in his hands, and he was looking down enough that Daniel couldn't see his expression. But, despite the shyness trying to creep into his voice, he spoke clearly enough that the archaeologist didn't have to strain to hear him. "You're not terrible at it." John glanced up and met Daniel's raised eyebrows with a small smirk. "I always thought you were pretty good at it… Still are."

Daniel smiled, chuckling lightly. "That's the same thing you said when I asked you to be careful before you came out here the first time."

John's smirk turned to a reserved smile. "I know."

Raising his eyebrows, Daniel's smile slowly widened. "See. It's coming back." He kept his voice optimistic and reassuring, but John's eyes turned downward again.

"Part of me wishes it wouldn't," he admitted so quietly that his voice was barely audible.

Daniel sighed heavily. Nodding, he replied softly, "I know."

A/N: Hoped you liked this chapter! I'll try to post the rest tomorrow, but my eyes are getting heavy so I'm gonna get some sleep. As always, reviews are greatly appreciated!