AN: So, here we are. Started writing this second half while I was still halfway through the first half. Can't believe I managed to get this far with this story actually, I'm quite impressed with myself.

One small note before we begin: there was a tendency reviews to be left that were unsigned but had very specific queries/issues with the story that I felt required a reply, however doing so in Author's notes cluttered up the story and artificially inflated the word count, something I intend to avoid as much as possible in this story. Without wishing to be ungrateful for detailed, engaged reviews, I ask that anyone reviewing with detailed queries or points please sign in with an account if possible so I may reply to them personally. I hope this is not unreasonable.

Anyway: I hope everyone enjoys the sequel. :-)

Prologue: Death Of The Normandy

The woman was young, or at least young looking. Her hair was long and dark, her face beautiful in a classic kind of way, and her figure was slim and curvy in the right places, only emphasised by the body-hugging black, grey and purple uniform she wore. Her voice was calm and measured, but the scepticism with which she approached the entire topic of her conversation remained steadfast.

"Shepard did wonders for Starfleet. He basically saved an entire foreign government, putting them in our debt in the process. But for all that, he is only one man."

"I know." The man's voice was sharp contrast, cold and calculated but dynamic as well. His hair was short and grey, his face lined with many years worth of cares. His uniform was red, grey and black, with gold decorations as befitted a man of his stature. "But that one man is our best source of intelligence on the Reapers."

"His history with us makes it unlikely he'll help willingly, you do realise that." She was to trying to be insubordinate, she was merely stating facts.

"Then he helps unwillingly," the man replied sharply. "I only need his help, not for him to be all smiles and cheerfulness when he does it. I outrank him. Worst comes to the worst, he'll have to follow orders. Besides, his experience with us is Reed, and Reed will be working under his command."

The woman nodded, understanding his reasoning. "I still can't believe they're making the Normandy do such boring, routine patrols. They aren't going to stumble onto a new Borg invasion by flying around scanning random systems."

"We know they won't, but they don't. At any rate, the patrols are mainly to appease the Council races, not because Starfleet thinks they're any good. We both know that appeasing the Council races is important, especially given their strength. We need them for the war - for more than one - much as we may not like some of the political requirements for that help." The cold words demonstrated the cool intellect the man commanded, as he calculated the maximum potential strength and benefit that the Council could add to any war with the Borg versus the possibility of success without them. Such calculations were his stock in trade, the thing that made him a formidable leader, and sometimes she was in awe of them, and him. Sometimes, though, he terrified her with the extent of his ruthlessness - an extent that surpassed anyone else in this organisation.

"What about our strength?" the woman asked softly.

"That rather depends on the shipyards, doesn't it." The question was implicit, without needing a real voiced answer (since he probably already knew exactly how well the shipyards were doing), but she knew him well enough to answer it anyway, just to be absolutely certain.

"We're building ships as fast as we can, and there's always crews, so we're getting it done, slowly but surely. I only hope it will be enough when the Borg - and the Reapers - show up again."

Confidence now filled the man's voice, confidence born of more planning and forethought than was strictly necessary even for a worst case scenario - just how Admiral Jack Harper, Starfleet officer and current head of Section 31, liked it. "We will have Captain Shepard, and the best fleet in the galaxy. It will be more than enough."

Although he had perhaps not had the best time while commanding the USS Normandy, given her heavy involvement in the recent Borg incursion and several major battles, Captain John Shepard thought with a vaguely proud - if tired - smile on his face that he had made a reasonably good accounting of himself as her Captain. She was - or rather, had been - an Ambassador class starship, her elegant swan neck and beautiful blue main deflector set into the stardrive section, under a beautiful round saucer section that shone silver-grey in the starlight. It was a shame, he thought to himself, that this service was about to end like this, and more a shame that he was about to die and not be able to relive it in his memories.

It was funny. He had woken up this morning in a surprisingly good mood, feeling as though everything would go well today. He had shaved his stubble for once, deciding to go with the clean shaven look. He had even smoothed down his somewhat untamed hair - he'd been letting it grow out these last couple of months, letting himself get more at ease with being the Captain of a starship. The effect was messy but worth it.

The Normandy's most recent orders had been to fly around some outer sectors of Federation space, performing what were essentially dull patrol duties, or as Jeff Moreau (commonly known as Joker), his helmsman, preferred to refer to them, "the milk run from hell". Boring, but nonetheless useful: these patrols were ostensibly keeping an eye out for any signs of a continued Borg presence. Although their defeat at the Citadel - and the destruction of the Reaper Sovereign - had been a blow to their enemy, Shepard and Starfleet command both knew that continued Borg presence was a real danger, and so Shepard had agreed to take this patrol run. Secretly though, he knew it wasn't the greatest danger - that lay elsewhere.

The Reapers. Starfleet Command had believed him - they weren't fools - but they were sceptical about the buildup of forces Shepard recommended. They were always less than thrilled about military buildup. It couldn't be helped. Anderson was confident he could convince them - but that still left the milk runs.

That morning, he had been in his Hazard suit down in the Holodeck, running some training simulations with Garrus Vakarian, his turian security officer. Garrus had taken up Shepard's offer of a permanent post on Normandy after the Battle of the Citadel, unlike Wrex (who had decided to return to his people, or Liara, who had returned to her studies of the Protheans), and had become a permanent tactical officer and security chief. He had also taken to joining the Captain in his training sessions.

The Holodeck - one of four on the ship - was one of Shepard's personal favourite tools for training, leisure, and sometimes - as it had been that morning - catharsis. He and Garrus had run a simulation recreating the attack on the USS Enterprise, some three years ago, in which the Borg had invaded the ship and assimilated many of it's crew. Shepard had taken to reliving old battles in this way only recently, mainly as a way of taking revenge on the Borg - he knew if he didn't let these feelings out, they might compromise him when it really mattered, and he couldn't let that happen.

He knew feelings of revenge might not be up to Starfleet's strictest moral standards - nonetheless, he had to admit to a certain level of enjoyment in taking the simulated cybernetic bastards down with an equally simulated TR-116, a luxury he had never had during the real events.

He took down another holographic Borg drone with his TR-116, smiling at the sight of it's head exploding. He checked the weapon again, and nodded to himself.

"I think that's all of them, Captain", Garrus said from behind him. He leant against a bulkhead. "You know, I wish I had a few of these. There's a couple of cases I went through during my time at C-Sec that would have been really nice to handle a little differently."

"Such as?" Shepard asked, his curiosity piqued.

"Eh," Garrus grunted softly. "Nothing that interesting. At least, not right now. Most of it's been dealt with. Old grudges and all that."

Shepard nodded. He knew the feeling of keeping old grudges. Hell, they were standing in a replication of one.

"Grudges can be a good thing, Garrus," he said softly, "provided you don't let them consume you. That's why I exorcise my demons here."

"I have no intention of letting them interfere with my work, Captain," Garrus said a little too formally. He did that sometimes - probably an expression of turian military upbringing. He would become a little too formal, as if taking a comment too seriously.

"Captain," the voice of Commander Charles Pressly, Shepard's CO, came through the comm system, interrupting the Captain's response.

Shepard tapped his combadge. "Go ahead, Mr Pressly," he said.

"Hate to disturb you sir, but we've finished our sweep of this sector and are moving on to the next," Pressly informed him. "I thought you'd wanna be present."

"Understood," Shepard replied. "I'm on my way now."

He turned to Garrus and shrugged. Garrus returned the gesture, and together, Shepard still in his Hazard suit, the two walked off the Holodeck and headed for the bridge.

Once they got there, Pressly gave up the command seat with a soft smile. He was a slightly older man, with a goatee and a receding hairline. "All yours, Captain," he said, moving to an auxiliary station nearby that he usually sat at when or being called upon to hold the bridge.

Shepard sat down in the command chair, and began reading over a ship status report summary a crewman handed to him. Nothing seemed too out of the ordinary - Normandy tended towards being more reliable and efficient than the average Ambassador class starship, a combination of many different factors.

"You heard about the Dominion?" he heard Joker say to Kaidan Alenko, Shepard's Ops officer, as he inputted commands into his console. "They're making noises about war."

"Of course they're making noises," Kaidan replied dismissively. "They've wanted a war for years. Only thing stopping them was the presence of the Citadel Council on our side."

"So why now?" Joker asked.

"Combination of our losses and the Citadel's," Kaidan explained, frowning softly. "Plus I heard they might have been building up themselves."

"You seem awfully well informed, Mr Alenko," Shepard interrupted, a teasing smile on his face. "Secret SI plant, are we?"

"No sir," Kaidan replied with an easy grin. "Just motivated to do my homework. We're in enough trouble with the Borg without some other alien empire choosing now to start a war."

"Ain't that the truth," Shepard sighed, sitting back in his chair. The Dominion situation was one he had been briefed about by Anderson and others, including Admirals Ross and Hackett. It was a worry - not that they couldn't defeat the Dominion, troubling though the projections for any conflict were - but rather that they'd be too busy fighting a war with the Dominion to be able to fight against either a renewed Borg invasion or worse, against the Reapers when they finally came.

"So tell me, Mr Alenko," he said, shaking these grim thoughts off. "Is this system any less of a boring patch of nothing than the last three systems?"

In reply, the Ops officer pulled up a list of statistics onto his station.

"Twenty five million particles of space duster cubic metre on average," Kaidan recited, "with an asteroid belt, and a class four comet flying through. No inhabited planets. One class M, early-ish stage of development."

"Early-ish?" Joker snorted. "That a technical term?"

"Yup," Kaidan smiled back. "Acceptable scientific label. Followed by the middleish, and the endish."

"And where's Earth?" Joker asked, a wry eyebrow raised.

"Probably in the middle-ish," Kaidan said with a shrug and a wry grin of his own.

Shepard basked in this - the camaraderie of a team at work. In all his years, he had never had an experience quite like being the a captain, getting to command the machine instead of being the cog, but more importantly seeing the cog at work from outside, it was wonderful.

Little did he know it was all about to end.

"Captain," Garrus said from the tactical station, his hands flying over the console, "I'm picking up an unknown signature, coming in from the edge of the system. It's on an intercept course -"

An explosion shook the bridge, and a second. For a moment, for Shepard at least, the world went black.

Shepard's world was nothing but darkness for what felt like an eternity at the time - in retrospect, a rather funny thought, given what was about to happen. When he finally he woke up, for a moment he didn't know what had happened. Whatever had hit the Normandy, it had hit them with such force that it caused several overloads in the consoles, leaving people dead and injured around the bridge and smoke in the air. Shepard had been thrown out of his chair by the force of the impact, and groaned as he realised he had bruised several ribs in the process. Near him, Pressly was down, the nasty, bloody tear across his jugular and the shrapnel lodged in his eye more than enough to convince Shepard that his redoubtable XO wasn't going to be getting up again. Cursing at losing a good officer - and more importantly, a good friend - Shepard pushed himself to his feet.

The bridge was wreathed in smoke and flame. A lot of people were down - too many.

"Report!" he called. There was no answer, and he snarled slightly. He couldn't deal with no answer, not right now. "I said report!"

After a moment, Kaidan appeared out of the smoke and fire. There was a gash on his forehead but he was otherwise unhurt. He struggled to get to his station for a moment, and finally got into his seat. Next to him, Joker was wrestling with the helm, trying to keep the ship level.

"We've been attacked - whatever hit us, it took out eighty percent of our shields and tore through our hull, which knocked out most of our main power reserves," Kaidan reported, his face a mask of worry as he frantically inputted commands. "Dammit! We're venting atmosphere - and crew!"

More death. Shepard cursed softly under his breath. He hated losing people under his command, and since he had become Captain he had lost thirty six people, many in battle against the Borg - including Ashley Williams.

"Helm control is gone," Joker reported, sounding oddly calm given the situation. He was clearly trying to regain control somehow.

"Any idea what hit us?" the Captain asked his officers.

"I think it was some kind of concentrated particle beam," Kaidan replied, checking his sensor logs. "But I can't be certain."

Shepard frowned - a concentrated particle beam? Sounded like the weapon Sovereign had used on several Starfleet ships during the Battle of the Citadel, but he had to know for certain. "Can you tell me what..."

"Captain!" the voice of Tali'Zorah vas Normandy, Shepard's quarian Chief Engineer, came through the comm system, cutting him off. She sounded worried and frantic. "That hit seriously damaged our warp containment field, and it fused our ejection system."

"No way to override?" Shepard asked, realising what this meant.

"None sir, they knew exactly how to hit us," Tali said grimly. "I estimate we'll have a warp core breach on our hands within the next six minutes!"

"Shit!" Shepard swore, thinking quickly. "Where's the hostile?!"

"No sign of him, though sensors are pretty beat up," Alenko said, tapping out commands on his console. It mostly failed to respond. "He might have shot us up and run."

"That'd be clever," Shepard said grimly. There was no chance of the hostile getting caught in the warp core explosion this way, and there was no need to deal any further damage with the containment rupture. "Alright, let's get the hell out of here." He tapped a command on his armrest console. "All hands, this is the Captain. I am initiating General Order Thirteen, we are abandoning ship. Report to escape pods and shuttles."

Kaidan and Joker turned to look at Shepard. Neither of them had expected him to order an abandoning of the ship, even with the damage they'd sustained, but he looked pretty serious. Slowly, Kaidan got up, and headed for the escape pods, joining the few other bridge crew still alive. Joker on the other hand stayed resolutely where he was, anger on his face. He returned to his console, trying to get it to respond. For the moment, Shepard was content to let him do so. He made certain that every other crewman was off first, triple checking the launch protocols of the shuttles and escape pods as they went.

Eventually, it was only the helmsman left on the bridge. He was still messing with the console, clearly still trying to keep the ship going somehow.

"Joker, move!" Shepard yelled.

"I'm not leaving," the helmsman replied stubbornly. "I won't abandon the Normandy."

"And precisely what are you going to do that can save her?" Shepard asked. "She's suffering a core breach!"

"I can save the saucer section," Joker replied, desperately. "Try and get as far away from the explosion as we can."

It would have been a viable plan had they retained crew, but everyone was off by now. Besides, there wasn't enough power for saucer sep left.

"Joker, we have to leave," Shepard said.

"No, I can save her!" Joker replied angrily.

Shepard cursed, and went to the tactical station, accessing the transporter systems. There was enough power left for maybe one transport, for one person.

"What are you doing?" Joker asked, not turning to look at the Captain.

"Saving your ass," Shepard replied - he had found an escape pod that was launched. Joker apparently realised what Shepard was doing a half second before he did it, and got up to protest - but by then it was already too late, and Joker had been beamed away.

"Right," Shepard said. He checked everyone was off - according to the internal sensors, he was the last life form aboard. Unfortunately, all the escape pods and shuttles had left too, and he'd just used the last power the transporters had left.

"Damn," he swore. Now he did have to separate the ship. He jumped down to the helm station and began inputting commands frantically. Fortunately, the power for life support was still present - just. Shepard quickly began re-routing all the power he could from life support, trying to get enough to jump start an emergency saucer separation. Finally, he manged to get sufficient power to have the ship begin the separation sequence. Shepard heard the clang of the sections separating reverberate through the ship, and smiled softly, as he inputted a command to move the saucer section away from the doomed stardrive section. It responded - albeit sluggishly, given the low power - and he smiled as it moved. Maybe he would be able to save something of his ship after all.

A few moments later, Shepard grabbed onto the console as the entire saucer section shuddered under an immense shockwave. More consoles sparked and Shepard was certain at least some of the inertial dampeners had gone offline. Still - he was alive, and there was something left of his ship at least. He found himself struggling to breath.

"Warning," the computer said, interrupting his thoughts. "Life support offline. Vessel unable to support life."

Cursing as he remembered the shunted life support power, Shepard retrieved his pressure helmet from his Hazard suit transporter buffer, and sealed himself in. There was enough oxygen in the suit's storage to keep him alive for a few minutes even after the Normandy's life support totally failed.

He looked up at the static-distorted viewscreen to check the space around him - and froze.

That ship must have been the hostile: it was huge, vaguely cylindrical, and it seemed to be made at least partially of rock. It was heading straight for the Normandy, and the Ops station, though it's sensors were all but dead, could still confirm that it was charging weapons. Shepard quickly tried to move the saucer section, enact some kind of evasive patter - but it was to no avail. There was no power left.

A bright yellow particle beam lanced out, crashing into the saucer section. It sheared diagonally across the surface of the hull, splitting the saucer in two. Shepard swore as the structural integrity of the bridge failed, the hull breached, and he was sucked out into space.

Suddenly, he found himself floating in space, his Hazard suit protecting him from suffocating as he floated out into the void. Even as he thanked the stars for his luck, he heard a sudden hissing - and the sound of his suit expelling atmosphere into the void reached his ears, which widened with the realisation that he was about to die.

His life flashed before his eyes - his crew, his friends, his ship - and he had time for a moment of reflection on the events that had led up to this.

His last thoughts, as his lungs burned from decreasing oxygen and his brain started feeling cloudy, were sadness at losing his ship, and regretting that he wouldn't be able to serve Starfleet against the Reaper threat when it finally came.

"I have good news and bad news," she reported, hands clasped behind her back.

"Bad first," Harper ordered, reading a report as he did so.

"Shepard's ship was attacked and destroyed. We suspect the same individuals responsible for several missing ships. We're working on leads."

"Shepard's status?"

"Reported deceased."

Harper's eyes flicked up to her, coldly assessing her body language.

"The good news?" he asked.

She smiled softly. "We recovered the body after a short while - estimated twelve hours of death. We're preparing the contingency plan. Currently estimating several months for cellular restoration - we won't know the exact number until we undergo a complete exam - with another few for any modifications. Best guess - two to three years out."

"Then we'd best hope we don't need him before then, hadn't we?" Harper said, a wry smile on his lips. "You know what you have to do. Carry on Lieutenant Commander Lawson."

"Aye sir," Miranda Lawson said, nodding formally. She turned and walked out of the Admiral's office.

She had work to do.