This diverges from nBSG canon during Exodus Part 2, but several things are still intact, the identities of the final five chiefly among them. Point of divergence should fast become apparent.
Yes, the premise isn't exactly new, but I want to give it my own spin, because the other side of this is original. At first this may seem like a wish-fulfilment story, but I do have a plan for everything you will read in this part, but be warned beforehand, I will take some liberties with the timeline, especially concerning the events of "Crossroads".
Season 4? What is this Season 4 thing of which you speak?
Don't belong to me, just taking them for a ride. The first time I write for nBSG.
The Long Road
Colonial Battlestar Galactica (BSG-75), over New Caprica
The Combat Information Centre of the Colonial Battlestar Galactica was thrown about again when even more Cylon ordnance impacted on the ship's armour.
"Status on the FTL drive?" Admiral Adama yelled, struggling to be heard over the organized chaos that surrounded him.
"Five minutes at least, Sir!" someone replied, and Adama realized then that he would not get his ship, or those left on the planet out in one piece.
Another explosion rocked the ship, and someone was yelling something, but drowned out by the sparks flying.
"I said," the Communications officer coughed away some of the smoke and repeated, "it was the Pegasus!"
Adama's head whipped around to the DRADIS readouts, and for one he was glad that someone had disobeyed orders. Outside, in space, the second Colonial Battlestar fired her forward missile launchers. Not expecting an attack from literally behind, the Cylon Base Star was unable to intercept them, and the two salvoes of two thermonuclear devices each turned one half of it into molten slag and the rest of it into a grave. While she made a 'by the skin of our teeth' pass on a second Base Star, her Defence Batteries let loose.
Like it's Colonial counterpart, the Base Star's hull was lined with armour designed to defeat the other side's weapons, but at this range, hits into the various weak points, such as the hangar bays and sensor systems were unavoidable, and in the fifteen seconds it took the Pegasus to pass, only few shots were fired at her, while the Base Star was crippled, at least enough so that it would not matter for the remainder of this battle.
Pegasus fired her forward launchers again, but the Cylons on the two remaining Base Stars were alerted now. Much to their surprise, the nukes were not set to detonate against them, but rather between them and the fight, so seconds before they would have been intercepted, theirs and the Colonial sensors were blinded.
However the Colonials had one advantage, the crew manning the Pegasus had known what was going to happen and the crew and fighters of the Galactica had been warned at the last moment on the tactical frequency. Still, some died or were permanently blinded.
By the time the Cylon DRADIS showed anything again, the two Battlestars had adopted a staggered formation, with the Pegasus partly shielding the older ship against fire, and not by coincidence the more damaged sections. This forced Galactica to cease fire with part of her guns, but this was more than compensated for by the presence of the second ship.
Even so, the Cylons were beginning to overwhelm them, and when the Colonial Fighters disengaged...
By the time they realized what was going on, more than half of them had already landed, and before they could re-group to overwhelm the defences of the two Battlestars, the Colonial ships vanished in the bright flash of their FTL drives.
The actual party had waited until the fleet had executed two consecutive jumps, and even then Admiral Adama and was more interested in taking up stock of what they had lost. Hundreds had been left behind, both the Battlestars had suffered significant damage which would take weeks to repair. If one had a drydock that is, for them it would take even longer. Still, Galactica had taken less damage than if Lee had followed his orders...
A knock on the hatch to his quarters made him look away from the reports on his desk.
The officer looked different from when he had last seen him, and the ashen, almost defeated look on his son's face made him forget protocol. Nothing like the end of the world to teach one the right set of priorities.
He rose, stepped around the table and hugged Apollo tight.
"How are you holding up, son?"
Apollo sighed and sat down in the chair opposite his father's.
"I've been better. Not sleeping much doesn't help."
Adama looked at his son, and all things considered, Apollo was in better shape than he had been years back when his mother had died.
"For what it's worth, I know what you are going through..."
Before the attack on the twelve Colonies this comment would have drawn a biting retort, heated words and slamming doors, but Apollo had gone through the same process as his father.
"I still see her face every time I close my eyes, dad."
Adama was at a loss for words, but the look on his face and in his eyes told Apollo just that.
"When that display bank fell, she looked at me. Dee looked right in my face when she died, dad. I don't know how I am supposed to live with that." he said, cradling his head in his hands.
Adama sat down himself. "I can't tell you that, Lee, but..."
Apollo looked up, and the ghost of a smile ran over his face. "Thanks anyway, Dad. I appreciate it."
With that, he pulled on his Commander's persona and reached for a uniform pocket, taking out a leaf of paper.
"The damage to the ship could have been worse. Pegasus has.." he paused, swallowing, "three dead and forty-seven wounded of all categories. My CMO thinks that of those two will die within a few days, the rest should recover. Pegasus has lost half a dozen Battery guns, which we can replace from stores, and my...XO... says that the manufacturing plants will be online by this afternoon, so by tomorrow we can start to replace our Viper losses. The chief says the other repairs will take a couple of days, but the ship can jump and launch Vipers."
Adama nodded and knew that Pegasus hat gotten off lightly. In their few conversations between then and now he had gleaned that Lee had had the desperate idea to ram his ship into one of the Base Stars, had the Gods not smiled on them and placed the final jump co-ordinates behind the Cylons so that Lee had been able to surprise them the way he had.
"Very well then, Commander."
Apollo handed over the papers that contained the more detailed damage report he'd read on the shuttle ride over. Some thirty minutes later he was rising to his feet and stepping through the hatch. He barely managed to make it to the hallways outside the pod where his shuttle was docked before near-collapsing against the bulkhead.
He had to make it aboard, because there were any number of people he did not want to see him like this, especially not..
"Lee, how are you?"
Perfect, frakking perfect. Just the one person he least wanted to see right now.
"Captain Thrace, what can I do for you?"
If Starbuck had decided to take offence at his brusque tone, she did not show it, instead she grinned and placed herself beside Apollo on the other side of the hatch.
"Nothing much, Commander." she said, putting obviously insolent emphasis on the rank.
Ah, there was the Starbuck he knew. However, he had too many problems of his own to let the bite catch.
"Well then, I will return to my ship then." Saying no more, he turned, opened the hatch and stepped through it, closing it behind with a bang that to Starbuck had the sound of finality.
But instead of doing what her instincts told her and following him through the hatch, she silently cursed and banged her fist against the metal of the bulkhead, making the hallway reverberate with the sound. "And to you too, Lee." she said and stalked away.
She hadn't seen that the Admiral was standing at the next intersection in the other direction, sad that his two favourite subordinates has moved so far apart. But, there was a reason why he was in this corridor.
Sickbay was still overflowing with those that needed aid, but Cottle had still managed to get a sense of order into the whole mess, with his medics conducting triage and treating the lesser wounds while he and the only two other civilian doctors on the ship handled the more severe cases. Adama knew that a similar arrangement was in force aboard Pegasus, but he doubted that Lee had been able to force himself to visit there more than once since the battle.
One of the few semi-private beds, set apart from the rest of sickbay by a few screens, was occupied by someone else he really had to talk to. Adama nodded at Cottle, but hesitated at the threshold. The last time he had talked to Sharon Agathon it had not gone well. In spite of being the best Raptor pilot on either of the Battlestars under his command, she had still forgotten military discipline when coming face to face with the Admiral. Standing on the other side of the bed that held her no longer comatose husband and with her long thought to be dead daughter in her arms, she had accused the Admiral of deliberately deceiving her, not believing him when he had truthfully told her he haddn't known. In the end he had followed Cottle's 'suggestion' and left sickbay. Two hours later Halo had woken up.
"You know that I shot her for saying that you had lied to me?"
Adama was startled to find that she had heard him. He pulled the curtain aside and stepped through, closing the gap behind himself. The scene was similar to what he had seen the last time he had tried to talk to her, only that this time the baby was awake and playing with a rattle that someone had made for her out of discarded Raptor parts.
"I believe you, Sir." she said, without looking up. "I didn't know if you had lied to me or not, and had no way to tell, but isn't this what trust is?"
Recognizing his own words from what seemed to be so long ago, Adama stepped closer and looked down at the still form of Karl Agathon.
"What happened down there?"
Sharon snorted. "It was when I went to get the codes. They all didn't recognize me, the Centurions and the even the humanoid models. But then in that room, when that...thing told me that you had lied to me, I...I lost it, Sir."
She looked up and her face made it clear that she was seeking his forgiveness.
"I shot her, Admiral, right between the eyes."
Hera had probably been sensing her mother's distress, but she calmed down quickly, and Adama was granted the opportunity to observe the only Cylon he trusted with her child.
"I had the codes, but instead of following the plan, I just ran through the complex and the camp, searching for my daughter. If not for Felix, I..."
Adama knew this story from Gaeta's end. How he had seen a frantic Sharon Agathon ransacking the offices in the complex, how he had forced her to give him the codes when she had refused to leave without her daughter, how he had seen her run off, throwing the chip with the codes at him almost in an afterthought.
"What made you believe her, Lieutenant?"
"It was the first thing she said when she recognized me. 'He lied to you, you know. They don't deserve your loyalty.' She then told me where I could find Hera."
"Then..." But before he had finished the sentence he realized what had happened.
"I ever only half believed her until I stumbled over the tent. Pure chance, Sir. Pure chance. If I had taken a turn in the other direction, Boomer would have beaten me there."
"You met her?" Adama exclaimed, startling Hera into a small, thin wail.
When she had calmed down, Sharon looked up at him. "I hope there was no Resurrection ship in range, Admiral. I had the advantage of being armed."
It told Adama everything he needed to know and explained some of the wounds she still had on her face.
"But Admiral?" she said, sensing that Adama was about to turn and leave, "you didn't know. I truly believe that now."
"Thank you, Lieutenant."
Helo began to stir, so Adama merely smiled, nodded and turned to leave. Once he was out of sickbay, he sighed. One issue somewhat resolved, only a million others awaiting him.
Cylon Base Star, over New Caprica
The meeting room at the centre of the Base Star was not very full, only Caprica Six and a Five were present, the other humanoid models in the system were engaged in damage control efforts on the crippled Base Star or on the surface, while Boomer had yet to return from the Resurrection ship, which was stationed in a system two jumps away.
"Well, this was a frakking disaster, wasn't it?" Six opened the proceedings by stating the obvious. "We did not expect that the humans would delay jumping in their second Battlestar, nor that it would appear in a position so advantageous to them."
Five only snorted. "Oh come on, you don't believe this was by design any more than I do. The Humans were lucky, that's all."
Six pondered this, and then was forced to agree.
"Probably. Still, one can't help but note their... tenacity and courage."
"This wasn't courage, it was sheer desperation, nothing more."
"It may be, but the point is, they succeeded where they shouldn't have, and I, and my line, can't help but wonder what God's plan was for this world."
"I have faith that we will find out in due time." Five said, and Six knew that he was serious, "but at the moment the matter at hand is, what do we do now?"
"We do what we did since the fall of the Colonies." a new voice added itself to the discussion. It was a One, in particular the copy that had infiltrated Galactica only to be fired out of an airlock. "We hunt them, and we destroy them. Admittedly, it would have been easier to do that here, but they can run only so fast and so far. Even more so now that we have that pet of yours, Six."
"I still believe what I said when we first arrived here, Gaius Baltar will prove to be a valuable asset. He was their best remaining scientist, and he can be properly motivated to help us."
"Can you guarantee his loyalties? He is a human after all." Cavil spat and was surprised when Six answered with confidence that yes, she could.
"Humans don't download, so they tend to be very protective of the one body and life they have. I believe he can be properly motivated. Especially if we give him the option of remaining behind alone on this planet and say that the Colonials may have been forced to leave some behind too."
"Just what would he give us?"
Six sighed inwardly, and hoped that Cavil hadn't read it on her face anyway, "Aside from being the best expert on Colonial systems we have, he is...was, their foremost scientist. His knowledge and his training will help us when the time comes. He knows the humans better than any of us because he is one of them."
Cavil phased out as he consulted those of his line that were within range.
"We agree. For now."
"That still leaves us with what to do," Five said and called up a local star map on a viewscreen folding up from the console in front of him, "and since there's only about half a dozen systems within jump range, I suggest we send reconnaissance groups into each of them, some raiders, just enough to do a quick sweep of the area."
Six was about to say something, but Five raised his hand. "I know that they must have jumped right on ahead, but Galacica and, to a lesser extent, Pegasus were bleeding atmosphere and debris, and I doubt the Colonials managed to pick any of it up."
"So we should find some trace of them," Cavil replied, " and and can from there extrapolate their probably course, assuming they continue in the general direction they had taken before this whole mess happened."
The other Cylons in the room nodded, and Cavil could not help but add: "This time at least we will finish this. Once and for all."