Disclaimer: I do not own the characters, just the story I put them in.

Spoilers: Season 1- "Hathor", Season 3-"Into the Fire"

A/N: Takes place in between "Into the Fire" and "Seth"

Chapter One

"Daniel, now!" Colonel O'Neill yelled at the archeologist.

"Almost got it."

That was not what the soldier wanted to hear. They were under heavy fire and the Jaffa were close to cutting off their escape route.

Jack ducked under a staff blast cursing at the stubbornness of Daniel Jackson. This had to stop.

Daniel was pulling with all his strength to free a tablet from the ancient temple wall. It was important and he wasn't going to leave without it.

Jack came up beside him and tried to jerk him away.

"I almost have it . . ." the archeologist shouted, shaking the colonel off.

A staff blast hit just above the two men's heads, raining chunks of debris down on them. Coughing and sputtering, Daniel came up with a grin, having successfully extracted the tablet.

Jack, however, was not happy. Shoving the scientist in front of him, he began laying down cover fire for their escape.

"Carter, you and Teal'c go and secure the 'gate. We'll head the other direction to draw these guys off then circle around to meet you." O'Neill shouted in his radio.

Running flat out into the surrounding hills, both men made it away from the ruins. The Jaffa seemed confused by the team splitting up and decided to go after the other two.

So much for that plan.

Eventually they came into a clearing and both men collapsed. O'Neill popped up and scanned the area to see if they had gotten away. All was quiet. Turning his attention to the archeologist beside him, his anger doubled.

Daniel was sitting, staring at the tablet with a triumphant look on his face.

"Jack, this is so . . ."

He wasn't able to finish due to the heavy blow that landed on the side of his jaw. It was hard enough to not only knock his glasses clear across the small clearing, but it actually snapped his head back so hard that his bandanna flew off.

Before he could react in anyway O'Neill hit him again, even harder, sending him sprawling. Then, standing over the wounded scientist, Jack pulled out a zip tie and bound Daniel's hands. Picking up the young man's fallen bandanna, the colonel shoved it into the archeologist's mouth roughly.

"It is time for you to learn something, Dr. Jackson."

Hauling Daniel up by his vest, Jack shoved him over a fallen log, so that he was draped in such a way that left little doubt in his mind as to what was about to happen.

Daniel had never been so scared in his life.

Jack began talking to him, "Here's a history lesson for you. In many warrior cultures throughout time, it has been an accepted practice for an officer to 'dominate' a lower ranking, or in your case, lower civilian team member, if said person consistently disobeyed or blatantly ignored orders."

Daniel's breaths came in terrified gasps. He tried to look over his shoulder at Jack, but had his face smashed into the log. He could hear the other man take off his vest and toss it aside. Then Daniel felt Jack reach around him and unbuckle his belt and proceed to unbutton his pants, pulling them, with his boxers, down quickly.

The younger team member of SG-1 tried to scream around the gag, but only managed a muffled yell. He then heard the colonel unbuckle and take his own BDU pants down. Still with his hand on the back of the scientist's neck, forcing him down, Jack kicked Daniel's legs apart.

With his mind racing, nerves screaming, the archeologist again tried to move. He was rewarded with a knee to the balls. Again his scream came out a muffled yelp. He could hear O'Neill giving himself a hand job, preparing to 'teach Daniel a lesson'.

" . . . Mmmaack," Daniel tried to speak around the bandanna in his mouth.

A blow across the back of his head came with Jack's low angry voice.

"I didn't think I would ever have to do this to anyone. But you, Danny boy, just can't seem to get it through your thick skull who is in charge."

Daniel's brain was in overload. He desperately searched for something to get him out of this. If only he could talk. He was sure that Jack did not have sexual leanings this way. And he certainly didn't, despite the rumors that ran ramped at the SGC.

No, Daniel knew that this was exactly what Jack had said. Domination. Why did O'Neill have to remember that little piece of history?

The young man found himself praying that Teal'c or Sam would come back looking for them. He would die of embarrassment, but at least his dignity would be intact.

He felt O'Neill still for a moment. The archeologist heard him spit into his hand and then felt the head of the colonel's dick press against his ass. Closing his eyes tight, tensing every muscle in his body and trying to project himself anywhere but here, he heard O'Neill growl.

"Now you will know who you take orders from on this team, Jackson."

With that, an agonizing pain shot through Daniel as Jack rammed home. With every penetrating thrust, the colonel made his point clear.

"You will follow orders. You will not argue with me anymore. And you will never tell anyone that this happened. It is between an officer and his subordinate."

With that last statement, Daniel felt O'Neill unload inside of him. A short moment later, Jack leaned over Daniel and whispered in his ear.

"Do we now have an understanding?"

All the shamed man could mange was a slight nod and a whimper.

Jack pulled out of Daniel's ass and got dressed. Then he cut the zip tie off of the scientist's hands, letting him free to dress himself.

Daniel could hardly move with out pain radiating up his spine. He pulled the bandanna out of his mouth and proceeded to pull his BDU's up. Refusing to let the tears in his eyes escape, he would not look at the colonel. After Daniel got his belt buckled, Jack tossed him his pack.

"Move out."

Walking was almost unbearable for Daniel. Any time he had a misstep or if they had to jump over something, the pain was enough to cause his head to swim. Locking his jaw tight, he wasn't going to say anything. No way was he going to give that satisfaction to O'Neill. It was a short time later that he knew he must be bleeding, as his boxers were becoming uncomfortably damp. Shoving that thought aside, he just wanted to get home. And he didn't mean the SGC.

By the time they reached the 'gate, Daniel was sure the others would be out looking for them. But to his surprise, they were waiting by the DHD.

"Colonel, you get lost?" Carter asked with a smirk.

Smiling as if nothing at all was out of the ordinary, O'Neill replied, "Nope. Just had a little trouble with Rock Boy here, not wanting to leave."

Glancing at Daniel, Jack added, "We have an understanding now, though. Right?"

Daniel said nothing, only nodded. Sam caught the pain in his eyes however, then noticed his swollen and bruised jaw. Concerned, she went over to him and reached out to his face. He quickly pushed her hand away and moved passed her.

"Daniel," Sam grabbed his arm, stopping him. "Where are your glasses?"

Shrugging, he broke away from her grasp and waited for the wormhole to be established.

Once they were though and walking down the ramp, Daniel felt like bolting, but managed to restrain himself. The colonel met General Hammond with a cheery smile.

"Welcome back SG-1. Glad to see you all in one piece." The Texan greeted them. "Head to the infirmary for your post-mission exams, we'll debrief in one hour."

As this was being said, Daniel walked right passed everyone and left the gate room without so much as a nod.

Surprised by this, the general looked at O'Neill.

"What's with Dr. Jackson?"

"Ah, he's got himself a new doohickey to play with. Probably wants to get his exam done quick so he can study it."

The general seemed okay with this explanation, but Sam was not. She was worried by Daniel's silence and odd behavior. She decided to corner the archeologist after their physical.

When the rest of SG-1 appeared in the infirmary, they all noticed that Daniel was not there. Sam turned to Jack with a questioning look.

"Maybe he wanted a shower first." The colonel suggested.

Sam wasn't so sure.

Daniel never showed up during their physicals. Janet even questioned O'Neill about the absence of Dr. Jackson.

"I'm sure he will be along any time now. He was pretty hyped on that tablet thing." The Colonel replied.

When she was cleared to leave, Sam headed right to Daniel's office. He wasn't there, nor did it look as if he had been there. Next she went to the locker room. Again, he wasn't there and his BDU's were not in the dirty laundry bin. Now Sam was really worried.

Right before she went to the briefing room, she called down to Janet.

"Has Daniel come in yet?" she asked the doctor.

"No. In fact, I was just going to see General Hammond about that. This is not like him."

When Sam entered the briefing room, Jack, Teal'c and General Hammond were already there. She sat in her customary seat and waited for the general to ask where Daniel was.

She didn't have to wait long.

"Where is Dr. Jackson?"

Sam noticed the slight look of worry and what she thought was guilt on Colonel O'Neill's face when shrugged his answer to the general's question.

Just then, Dr. Frasier came into the room.

"General, I just called to the security desk topside. Dr. Jackson signed out an hour ago. The airman said that he looked frantic. He hadn't even changed out of his combats, and when he drove off, he nearly hit a supply truck on its way in." There was no hiding the worry in her voice.

"Okay, what happened on P2X-138? Colonel?" Hammond had his irritated voice going full fledge.

Seeming a little agitated, Jack did not look the general in the eye. "We took some heavy fire . . . Daniel got his tablet thing . . . We had to split up to make it back to the 'gate . . . Par for the course, Sir."

"If it was par for the course, Colonel, why is Dr. Jackson not sitting here right now?"

Carter had enough talk. "Sir, permission to go to Daniel's apartment and find him."

"Granted. And take Dr. Frasier with you. There may be something wrong."

The two women left right away.

****

On the trip to the archeologist's home, Sam told Janet about his odd behavior on the planet right before coming back.

"He didn't say a word, Janet. Wouldn't look at me, wouldn't let me touch him. The side of his face was swollen and bruised as if he was hit. I really think that something happened between him and the colonel. I had a feeling that things were getting a little tense with the two of them, but, I can't see the colonel hitting him."

Janet was quiet for a moment. "I'm not so sure, Sam."

"What do you mean?"

With a look of conflicting emotions, Janet replied, "I can't divulge anything, but I can tell you that there have been . . . questionable incidents concerning Colonel O'Neill before. But they happened so long ago, I can't really think that he would revert back to using brute force. Especially on someone I thought he considered a friend."

That statement slashed through Carter like a sword. The rest of the trip to Daniel's place was silent.

General Hammond fixed an icy glare at the two remaining SG-1 members. Again, O'Neill seemed to be very distracted, as if something was gnawing in the back of his mind.

"Colonel, I demand to know if anything has happen between you and Dr. Jackson." He growled at his 2IC.

Looking down at the table and drumming his fingers restlessly, he remained quiet for some time. Then he looked up into the General's face.

"Sir, Dr. Jackson and I have been having some . . . difficulties in the 'chain of command' department. I know that he is a civilian, but he is a member of a military team. I had some . . . rather harsh words with him before we got back with Carter and Teal'c. Just to set things straight."

When it seemed as though he was not going to elaborate more, Teal'c turned to him and said in a low, angry voice, "Did you cause the marks on DanielJackson's face, O'Neill?"

General Hammond had not gotten a good look at the archeologist with his hasty retreat from the gateroom.

"Teal'c, what do you mean?" He asked the Jaffa warrior.

"When DanielJackson got back to the 'gate, I noticed that he looked as if he had been hit. Then Captain Carter remarked that his glasses were missing. On the whole, General Hammond, it was as if DanielJackson had encountered something that had caused him great distress. I did not think that it was that serious until my reflections just now."

The general had heard enough. Looking at O'Neill, then motioning to an airman standing just out side the door, Hammond stood up and leaned on the table.

"Colonel O'Neill, you will be escorted to your quarters where you will stay until such time as I find out what happened. You are officially under house arrest." Nodding at the airman, he finished, "Dismissed."

****

Sam and Janet got off the elevator at Daniel's apartment. They hurried to his door and knocked. No answer. Not surprised, Sam fished his keys out of her purse. Janet looked at her incredulously.

"We all have each other's house keys, in case one of us is laid up in the infirmary for awhile." She answered the doctor's questioning look.

When the door opened, Sam gasped. The usually spotless home of her friend looked as if a micro-burst had hit it. Cautiously, they entered. Furniture, books, his precious artifacts, was tossed around the room as if someone ransacked the place. There was broken glass everywhere on the floor. Carter immediately pulled her M9 from the holster in the back of her jeans.

Janet followed the soldier quietly. Maybe someone had broken in, but that seemed unlikely since the door did not appear to have been forced. Carefully, the two women made their way further in. Janet patted Sam on the shoulder and remarked, "All the windows are open. It's freezing in here."

They did not find Daniel in the living room, so Carter turned towards his bedroom. The door was shut, and what looked like blood was smeared a crossed it. Carefully opening the door, Sam inched in with her gun raised.

Though it was getting dark, both of them could see well enough to find Daniel lying on his bed, dressed only in his boxers. All the windows in here were wide open as well and the light November snow was accumulating on the floor beneath them. The scientist was facing away from the door and did not move as they came in closer.

"Daniel?" Sam quietly said.

She rounded the bed and stopped short. Daniel's eyes were open, but unfocused and staring. In hand was his Berretta, with the barrel in his mouth.

Frozen in place, neither Sam nor Janet were sure what to do. They did not expect this.

Sam slowly moved forward towards her friend, handing her gun to Janet first.

"Daniel? Will you hand me the gun, please?" she asked in a whisper kneeling down beside him.

He did not move, but she could see that his eyes had focused now. Inching closer, Sam continued to speak in a hushed, calm voice.

"Please, Daniel. Give me the gun."

His eyes moved to hers. It took everything in her power not to react to the look he gave her. The fear, sorrow and pain were etched into every line of his bruised face. Seeing Sam looking at him in the condition he was in, Daniel began to cry.

Taking advantage of his breakdown, Sam reached for the gun and got it away. She laid it down and wrapped her arms around the broken archeologist as he sobbed uncontrollably.

Janet approached warily. She turned on the nightstand light and gasped, "On my God."

Her eyes went over every inch of his body. His feet were cut from the glass that was on the floor, slowly dripping rivulets of blood onto his blanket. There were welts on his back that Janet surmised were from a belt. What shocked her was the way the welts were placed indicated self-induced. Then see saw the blood on the back of his legs and butt. Right then she knew . . . Daniel had been raped.

Seeing the horrified look on the doctor's face, Sam gently unwrapped her arms from around her friend and stood to see what would make Janet turn pale. Upon the sight she would never forget as long as she lived, Captain Samantha Carter's rage kicked in full throttle.

Pulling her cell phone out, she quickly called the base.

"I need General Hammond NOW!"

Janet moved to Daniel's side and kneeled down to look him in the face. Placing a warm hand on his head, she smiled at him in a way she hoped was not conveying pity. Beside her she heard Sam telling the General to send a med team in a truck to pick them up. Without going into detail, she told him it was far worse then what Colonel O'Neill had let on.

When Sam hung up the phone, she went and closed all the windows and found some heavy blankets to cover Daniel with. Janet went into his bathroom looking for a first aid kit. It wasn't much, but at least she could clean some of the open cuts.

As Janet went about wiping off the blood and administering to his wounds, Sam sat with Daniel, running her hand through his hair and whispering to him.

"Daniel, can you tell me who did this to you?" She asked.

He only buried his face into the pillow.

Looking over at Dr. Frasier, she could see a rage was creeping into her face as well. She turned back to the young man with whom she had grown to love in a very short amount of time. 'Kindred spirits', Janet always said, when Sam would gush about how she and Dr. Jackson could connect on a level that no one else could.

"Daniel," she tried again, "If I ask you some yes or no questions, will you answer me?"

It was a long wait, but he nodded his agreement.

"Did you get captured on the planet?"

He shook his head no.

"Can you tell me what happened?"

He shook his head no.

Realization hit Carter, "Did the person that did this to you, tell you not to say anything or tell anyone?"

A long pause passed, and then he broke into sobs again, nodding his head.

"Daniel," Sam did not want to ask this question, and she definitely did not want to hear the answer she feared would follow, "Did Colonel O'Neill do this?"

No answer.

"Daniel, I need to know. Did Colonel O'Neill . . ." the words stuck in her throat causing her voice to crack as she forced them out, "Did Colonel O'Neill rape you?"

Daniel did not answer, but his body tensed so much that he might as well have screamed 'yes' at the top of his voice.

There was such anger in the two women's faces that when Janet's med team came into the room, they actually backed away from them.

In full doctor mode, Janet had them prep Daniel and get him into the waiting truck. She and Sam would drive back in Sam's car, to discuss how they were going to handle the situation.