"What do you mean, he isn't there?" Adama shouted at the marine who'd come back to the commander's quarters alone.

"I don't know, Sir. I just know I went to the brig and no one was there. No prisoner and no guard."

Frowning, Adama picked up the phone and called CIC. "Captain Adama is missing," he began.

"No Sir," Gaeta responded. "Colonel Tigh ordered him brought to Doctor Baltar's lab. I presume he's still there."

"Baltar's lab? What in the twelve worlds for?"

"Apparently Sir, he was accused of being...a...a Cylon."

Gaeta wasn't normally intimidated by his commander, but he knew this was going to produce a rather unpleasant reaction. In expectation he held the phone away from his ear as soon as he finished speaking.

"A WHAT?"

Gaeta's instinct proved correct, as he clearly heard the exclamation on the other end of the line.

Immediately Adama reined in his temper and lowered his voice, although he was still angry. "Mr. Gaeta, who onboard this ship would believe my son is a Cylon?"

"I don't know, Sir. I think perhaps you should discuss it with Colonel Tigh." Gaeta had no intention of repeating second-hand information to his superior officer.

Adama slammed down the phone and dismissed the marine.

Laura looked at him questioningly. "Someone has accused Captain Adama of being a Cylon agent?"

Adama shook his head in disgust. "Apparently so. I'm going to Baltar's lab to get to the bottom of this."

"I'm coming with you," Laura asserted. "We can't just have people making idle accusations like that."

Adama nodded and they headed through the hatch together.

Tigh had ordered Lt. Valerii to resume her duties and she had gladly departed from the lab. When Adama and Roslin arrived, the marines were preparing to take Captain Adama back to the brig.

"Would someone please tell me what the hell is going on?" Adama thundered as he entered the room.

"Apparently Apollo had a little too much time on his hands and he decided to concoct a few tall tales," Tigh responded.

"What does that have to do with his being accused of being a Cylon? And what do you mean, tall tales?"

"He accused Sharon Valerii of being a Cylon and she accused him back. I think the whole thing is ridiculous but too many people heard them. I just wanted to prove it was a bunch of crap before too many rumors started flying around," Tigh explained.

Bill tried to take this all in. He decided this conversation was best continued in private. "I want to see you in my office NOW, Captain. You can return to CIC, Colonel." He turned on his heel and headed for his office.

The marine escort remained with Lee as he obediently followed.

Laura Roslin wasn't sure what to make of all this, but she was sure Captain Apollo wasn't the type to "concoct tall tales." She followed resolutely behind the Adamas, leaving Baltar to shake his head at the absurdity of what he'd just witnessed and then turn his attention to what in the colonies he was going to do about the predicament he now found himself in.

When the Commander, Captain, and President reached the commander's quarters, Lee stood at attention, waiting to be allowed to explain everything to his father.

Adama dismissed the guard and studied his son. He could see Lee had noted Laura's presence, so he decided to address that issue first.

"The President and I have come to an understanding."

Lee was afraid to hope for a positive outcome for himself at this point, but he was relieved that his father was apparently not going to overthrow the government after all.

Laura spoke next. "I have resumed my rightful office, and there will be no legal actions taken against anyone involved in this...incident." When Lee made no response, she continued. "I have granted presidential pardons to both your father and yourself. You will not be charged with mutiny as you were acting in good faith to defend the Articles of Colonization."

Lee wasn't sure what to make of this. On the one hand, he was overcome with relief. He would not face court martial and all its potential negative outcomes. On the other hand, he was a bit perturbed. He made a choice that day on Colonial One and he didn't regret it. As far as he was concerned, Tigh was the one acting unlawfully. No one had mentioned pardoning him. Right now, though, all he wanted to do was explain what he'd seen to someone who would listen.

Unaware of his son's myriad thoughts, Adama wondered why he didn't make some response. Shouldn't he be pleased or thankful?

Lee belatedly realized the meaning behind his father's intent look. "Thank you, Madam President. I am grateful for your support and trust. I assure you it has not been misplaced," he responded formally.

"You are quite welcome, Captain Apollo," Laura replied. "Now, what is this about Lieutenant Valerii?"

Lee once again explained what he'd seen in the hallway. Laura listened with interest, considering his concern but Bill was not convinced. His brow furrowed.

"So you think that not getting killed by the Cylons means that she IS one? Lee, that's quite a leap. I can't help but share the Colonel's suspicion that you were grasping at something to put someone else in a worse light than yourself. Do you realize you have jeopardized that young woman's career and besmirched her good name?"

Besmirched? Lee thought to himself. This wasn't going as well as he'd hoped.

Bill continued, thinking of how Boomer had successfully completed a dangerous mission just days ago. She'd been a trusted member of his crew for over two years. How could she be a Cylon? "Did you consider that in the confusion of the moment that you didn't see what you thought you did? Maybe the centurions didn't see Sharon; maybe she avoided detection just as you did!" He came to stand in front of Lee. "You should have come to me with this privately, rather than accusing her in front of a group of enlisted men. Do you know what a rumor that a Colonial Warrior is a Cylon could do to fleet morale?"

Lee was starting to get angry. He hadn't intended to bring down fleet morale; he was trying to keep them all safe. Had his father forgotten the water disaster? Someone on the inside had to be involved and no one was ever truly found responsible.

"Commander, I had no intention of making unfounded accusations." Lee felt angry that he was having to defend his position.

Bill interrupted him, "But yet, that's exactly what you did. It wasn't that long ago that the knowledge that Cylons looked like us was a tightly guarded secret, for precisely this reason. We knew people might start accusing each other for the most insignificant things. I didn't expect to see it happen with my senior staff."

"Ahem," President Roslin cleared her throat loudly. It was clear that nothing productive was going to come of the remainder of this conversation and in fact, quite the opposite was likely to happen. She decided to put a stop to it before things got out of hand. She was rewarded by a dual set of Adama glares. Both men had forgotten she was in the room and weren't pleased to be reminded. She wasn't cowed, however. "Gentlemen, what's done is done. Tomorrow we will get the test results and then we can put this behind us. We need to focus on plotting the location of the Tomb of Athena so when Lieutenant Thrace returns we'll be ready to send a team there."

Only years of practice at maintaining a neutral expression kept Adama's jaw from dropping. He couldn't believe she brought up that frakkin' arrow. Not to mention Kara. And how could she even consider sending a team to a Cylon-infested planet to find some architectural ruin that may or may not even exist? However, he didn't want to argue with the President in front of Lee, especially now. Focusing on the first part of the President's statement, Bill addressed Lee. "We will have the test results tomorrow. I will expect you to apologize to Lieutenant Valerii at that time. Until then, you will not discuss this matter with anyone, is that understood, Captain?"

"Yes sir," Lee made the only response possible under the circumstances although he desperately wanted to ask if Lt. Valerii would be apologizing to him as well.

"Dismissed, Captain." Bill made it clear that the conversation was over. "Resume your post."

Lee saluted and left, feeling more frustration than relief. He wasn't under arrest anymore, but he seemed to have lost his father's trust. He wished he'd never seen Boomer with the centurions. If they'd been just a few moments earlier or later, he wouldn't have. He resolutely headed for his office, determined to carry out his duties professionally. He also recognized with some indignation that his father didn't want him to be privy to the conversation that was certainly going on right now about this mission to Kobol. But if Kara was still alive, if she came back and the mission actually became a reality, then he was going.

Bill turned to Laura. "You can't be serious about going back to Kobol! Have you forgotten what happened to the team that was sent there?"

"Of course not! But we'll be prepared this time. The first team was caught by surprise. Also the base star has been destroyed. There are only the remaining Cylons on the surface to worry about. With careful planning and a little luck, we can avoid those.

"A little luck?" Adama was aghast. "We'll need a hell of a lot more than that!"

Commander Adama pulled off his glasses and rubbed his eyes. He and the President hadn't really come to an agreement about the mission to Kobol. He still felt it was a bad risk and the chance that the map to Earth was actually there was less than remote. However, he had agreed to assign Lieutenant Gaeta the task of mapping out a probable location of the tomb based on scans they had made of the planet, and he was considering who would make up the team that would land on the planet, provided Kara ever returned. He wasn't putting a lot of thought into choosing them now, as it was all a moot point without the Arrow of Apollo. The President had agreed that if Lt. Thrace did not return, the mission could not take place. The timetable for when to stop waiting on her had also not been determined. Neither of them wanted to leave without Kara, for vastly different reasons, but both realized the fleet couldn't stay there indefinitely. They would reassess the situation in a week. If no contact was made by that point, Adama feared they would have to move on.

As Bill undressed and prepared for bed, he couldn't help but turn his thoughts to Lee. He felt that their personal relationship was on very shaky ground, and he was not at all happy about this latest incident. Not to mention that Lee didn't seem at all repentant about his behavior on Colonial One and hadn't even seemed especially happy about being pardoned. Bill had no idea where to even start with Lee on a personal or military level. He supposed he needed to coordinate this mission plan with Lee, but he wasn't looking forward to it. Kara would be the elephant in the room in any discussion of Kobol and neither of them had come to terms with her loss. He did know that much about his son. He decided that after they met with Baltar, he would hold a preliminary planning meeting with himself, Colonel Tigh, Gaeta, and Lee, and then he would report back to the President. He shook his head. Wasting time planning a mission that would never take place. What a mess, he thought morosely as he climbed into his bed. He finally fell into a restless sleep, wondering whether Kara could still be alive.

President Roslin had come aboard shortly after lunch. She and Commander Adama were to meet in Baltar's lab to see firsthand the results of the Cylon tests on the two warriors. Due to the nature of the reason for the tests and the subjects thereof, both leaders had a personal as well as professional interest in the results.

Baltar nervously straightened his clothing as the time for the meeting with Adama and Roslin approached. They had decided they would wait and view both results simultaneously. Baltar thought that was just a nice way to say they didn't want to get up in the middle of the night to get the first result. Of course, they didn't seem to mind that HE had to do so. He cleared his throat in anticipation of the little speech he would be giving. Despite all his mental preparation, he still started slightly when the door opened and the President and Commander entered, along with Colonel Tigh. I guess he couldn't stand to be left out, Baltar thought. Then the idea that the Colonel's presence was perhaps in his favor entered his mind like a sign from the gods. He took a deep breath and greeted his guests.

"Welcome! Well come in, I mean," he stuttered. "You're, you're early. I mean, just five minutes early. Not that that's a problem, of course."

"Gaius, do calm down," Six was suddenly at his side, wearing a sultry blue dress.

Ignoring Six, Baltar moved to the computer screen where the results would be displayed. He pulled up the first result. "I ran Lieutenant Valerii's test first, as…well… ladies first, and all that," he babbled. President Roslin rolled her eyes. He turned the screen where they could see the result. Green lines. She was human. Adama sighed. Of course she was. He didn't know what Lee had seen, or thought he had seen, but he hoped this would put an end to his son's concerns regarding the matter.

"Now, Captain Adama's result finished up just a few moments before you arrived. I haven't even had a chance to see it myself, in fact." A few keystrokes later and another result was displayed.

Bill had started to leave, forgetting that officially he should see Lee's result as well, until he heard Laura gasp. He turned towards the screen to see...red. That couldn't be right. He blinked hard and looked again.

"I hope you know what you're getting into, Gaius. He's never going to believe that his own son is a Cylon," Six warned.

"My goodness! This is...quite a shock! Well, it is for me, I can only imagine how much it is for you," Baltar prattled.

Adama was stunned. He had fully expected both officers to be proven human. "How is that possible?"

"I am quite taken aback myself, I assure you," Baltar spoke earnestly. "But you can plainly see the results. One is human, one is Cylon."

Adama's eyes narrowed. "Lee can't be a Cylon. He's my son."

"I told you he wouldn't believe it, Gaius. You're just digging yourself in deeper," Six warned.

"Well, yes, of course," Baltar responded to both Six and Adama. "I can only hypothesize that at some point, the Cylons must have captured the real Lee Adama and sent this copy back in his place. An ingenious way to infiltrate us, don't you think?" Baltar tried to sound authoritative.

"Very clever, Gaius!" Six purred. "But be careful that you don't say more that you should."

"Bill," Laura spoke quietly. "When we interrogated Leoben, remember how I said he told me you were a Cylon?" She was rewarded with a glare. Bill didn't want to think about that and HE was certainly NOT a Cylon. "No, hear me out," she continued. "He didn't say "Commander Adama" he just said 'Adama.' He said, 'Adama is a Cylon.' At the time, I assumed he was referring to you. But what if he meant Lee all along? Maybe he was telling the truth? He told the truth about us finding Kobol..."

"Why would he try to warn us, if - and that's a big if - if they had replaced Lee with a Cylon?" Adama interrupted disparagingly.

"Who can say why the Cylons do anything?"

"Bill," Tigh entered the conversation. "It would certainly explain his recent behavior." He left the rest of his thoughts unspoken. If the Cylons had replaced Lee then they could replace anyone.

Despite his initial skepticism, Bill was starting to accept the idea that this was a possibility, despite the horrific ramifications both for himself personally and for the fleet. His lips pressed into a thin line. "Colonel, contact the sergeant of the guard. Have him send a team of marines here at once."

Colonel Tigh nodded and stepped over to the phone.

Adama's head was spinning. He knew Lee was human, but what if Baltar were right? What if the person he believed was his son was just a copy of Lee? He would have access to all their sensitive tactical information. He could have killed Colonel Tigh on Colonial One. Perhaps he would have if Laura hadn't intervened. Gods how could this have happened, he thought. What am I going to do?

A few minutes later the door to the lab opened and Captain Adama and Lieutenant Valerii entered. They had been ordered to be present to receive the results. Lee did not miss the look his father was giving him. He wasn't late, was he? Boomer had gotten here just as he did.

"Lieutenant Valerii, you are free to go. Your test showed you are human," Adama announced.

Sharon smiled triumphantly at Lee, who swallowed hard and took a deep breath. "Lieutenant Valerii, I apologize for accusing you based on questionable circumstantial evidence. You are an asset to this ship and it is an honor to serve with you." He hoped that was sufficient to satisfy his father.

Sharon still had deep inner doubts about her true nature, which she couldn't deny after what she saw aboard the basestar, but as long as no one here knew the truth, then she was safe. She smiled at Lee, genuinely this time. "Apology accepted, Captain. I also apologize. I guess I just got carried away or something." She was unaware that Lee's apology was only due to orders and felt she should return the gesture. She also knew that she had no basis whatsoever for her accusation and was glad this was all over before anyone realized that.

Lee nodded at her, and they both turned to leave.

"Just a minute, Captain. No one said you could go." Adama spoke sternly.

Lee rolled his eyes before he turned around. He had hoped his apology had appeased his father but obviously he was wrong. If the commander was going to be all by-the-book today, Lee knew well how to play that game. He came to attention. "Permission to resume my post, Sir?"

"Permission denied." Adama glanced back at the computer screen which still displayed the lines of red. Gods it was true. His son had been somehow captured by the Cylons and they had sent a clone back in his place.

Lee was bewildered but protocol did not permit him to question his father's orders. He presumed he was still out of favor with his father and was being punished on some level. He was surprised when he a squad of marines entered and approached him.

"Sir, you're to come with us!"

"What?" Lee lost his grip on protocol for a moment.

"We have orders to bring you to the brig."

"On what charge?"

Commander Adama answered. "Baltar's test has revealed that you are a Cylon."

"WHAT? That's absurd! You know I can't be a Cylon, I'm your son for the gods' sake!" Lee appealed to his father.

"You're not my son. You're one of them." Adama answered solemnly.

"Put your hands behind your head!" one marine ordered as another came forward to handcuff the Captain.

Adama's face was as hard as stone. Lee was surely dead. For who knows how long. And he'd been living with this...thing...in his place. How DARE the Cylons do this! As if it weren't bad enough that they kill Lee, they tormented us with this copy, they infiltrated us so completely. "Take that thing to the brig," he ordered. He couldn't watch as the Cylon who bore the likeness of his firstborn son was hauled away.

Had his father just called him a thing? What's happening? How could anyone believe this? "Dad! This is crazy! I'm not a Cylon! Baltar's made a mistake! Dad! DAD!"

"That's what they all say," Baltar mused. "They all deny it." He shook his head in mock pity as Lee was dragged from the room.

Lee was completely flummoxed by the sudden turn of events. He knew his father was angry with him but he never could have imagined this. He stopped his protests as he was taken further down the corridor and was careful not to give the guards any reason to use excessive force. They were already being none too gentle as they escorted him towards the brig.

"That thing should be interrogated," Tigh stated bluntly. "We need to know how long it's been here. I doubt it will tell us what happened to Lee but we can try to find out."

Adama nodded resolutely. Then he cast his eyes downward, thinking of his son. How long had Lee been dead? Days? Weeks? Months? How could he not have known his own son had been replaced by a frakking Cylon copy?

"Bill, I don't think you should be there. This must be...hard for you." Sympathy wasn't Tigh's strong point, but any fool would have to know that finding out your child had been killed and replaced by a Cylon clone would hurt like hell.

"I hate to ask, Saul."

"You don't have to ask. I'll take care of it. I owe that toaster a thing or two, anyway."

Adama winced involuntarily at the toaster reference. He realized Saul was right. He couldn't watch that thing be interrogated. Hearing Lee's voice...he shook his head to clear that thought. No, he could have no part in it. At least he had the small comfort of knowing Lee hadn't really committed mutiny. It was all a Cylon plot.

"Find out what you can from it...then put it out the airlock," Adama ordered gravely.