Author's Notes at the bottom. I do not own The Last Ship.

Prologue

4 October 2014

Rachel Scott was cold. Very, very cold. But, like lots of things in her life at the moment, she couldn't afford the distraction of being cold, so she shut it out of her mind to focus on the task at hand.

They were so close.

Three days ago they had made a major breakthrough and yesterday they had successfully gathered some material from the primordial strain of the virus that was currently attacking the world. That was now safely tucked up on the USS Nathan James, but there had been a problem. She was just analysing the mass spectrometer results from the first sample when Quincy had told her that the other three samples they had gathered were contaminated and that they would have to come back today to gather more. She had almost screamed. They should have been heading back to the US that morning but instead they were back on the ice cap analysing drill cores. At least the mistake had allowed her to write up her notes ready for transmission and update her journal. Lots had happened in the last couple of weeks and she'd needed to write it up so that someone could follow up her work if anything happened to her.

However, with the samples they had collected today, she was now confident that they had enough to take back to the labs in the US and get to work synthesising a vaccine.

Finally, after four months digging around in the Arctic, seeing lab after lab, team after team, colleague after colleague fall out of contact, they could start heading back to the US. She hoped that there was still the infrastructure back home to come up with a vaccine. All of them couldn't be dead, could they? She had been in contact with Julius until two weeks ago when he had told her he was moving to a decentralised lab and would be in touch. But he never had been. She assumed that communication had just broken down and that was the issue. The alternative was just too horrific to contemplate. To be honest, it was Connie she missed the most. Friends were the new family after all, and to lose Brad and Connie within weeks of each other was nearly more than she could take. Connie had dropped off the grid just like Julius. There one day, gone the next. Rachel prayed that Connie was still out there somewhere. She couldn't bear the thought that her best friend was gone.

While it would be great to get out of the cold and get back to the ship, she wasn't looking forward to her reception there. For the first four months of the mission the crew had been friendly and outgoing. For the past few days they had been surly and taciturn, obviously taking their direction from their Captain.

She supposed she shouldn't be surprised. It probably didn't take a rocket scientist to work out that she was the reason their mission had been extended after their weapons tests were finished. While a small part of her mind had noted, when they met at Norfolk, that the Captain was quite aesthetically pleasing, it wasn't something she could focus on. And with the importance of her mission she had barely seen him in the past four months. In fact, she had spent more time co-ordinating transport with XO Slattery and Lieutenant Green, the commander of their escort. She'd hoped Chandler wouldn't be a Mark One Military Neanderthal, but their conversation three days ago had suggested he probably was. She knew she'd come on a bit strong, but her mission was absolutely vital and the Captain had not needed to be as sarcastic with her as he had, in her view.

At least the new National Security Adviser had acted quickly to extend the mission, although the new orders clearly hadn't pleased the Captain. But she knew that the Captain was going to be even more pissed off than he already was when he found out the reason for the mission extension and the radio silence. She didn't blame him; she would be in his position. But she was under clear orders from the President of the United States, via the Pentagon, to keep quiet about the Red Flu unless she felt her mission was endangered and there was no contact with the US. If that was the case she was entitled to give him the sealed orders which were currently sitting in her safe in her cabin. Hopefully it would never come to that.

"OK Quincy," she told her partner, sitting up and stretching her back, "I think we're about finished." Although not her usual partner, Quincy had done OK on this mission. With degrees in geochemistry and avian biology, as well as virology, he was much more suited for this study than her long-time co-worker Dr Bradley Dickens, which was a good thing because poor Brad had been killed in a car crash in Washington DC four days before they were due to leave for Egypt. While Quincy had worked in and around her team for nearly ten years, she did miss Brad who always went out in the field with her and who she felt was much more attuned to her thought patterns than Quincy. She took a second to remember Brad and it was then that she heard it.

"Do you hear that?" she asked Quincy, looking around.

"What?" he replied.

She looked around again. "For a second, I thought I heard a chopper," She wondered if maybe Captain Chandler had finally lost his temper and decided to clear them off the ice again. She started to pack up the samples into the two separate sample bags.

Lieutenant Artur Dmitrievich Voronov watched the woman start to put her stuff together through his sniper scope. When the Admiral and Captain had briefed the attack yesterday the initial plan had been to fly right in, but the more he thought about it, the less he liked it and after the bad weather yesterday had scotched the attack, and their agent on the American ship had arranged for the scientists to come back again today, he had suggested to the Captain a two-pronged attack. Which is why he and Boris Romanovich had been dropped off eight hours ago and had walked in overland. And it was a good thing too. They hadn't expected to find a SEAL team with a dog guarding the scientists.

But there was nothing Artur could do about that now as they had to be radio silent until the attack. He and Boris were still out of range of his rifle but the idea was that the helicopter attack would flush the Americans towards them and then they could take their shots to disable one or both of the scientists. He would need to do something about the dog as well. It was just as dangerous as any of the SEALs. In the mean-time he just needed to wait.

He wondered if his wife Lydia and his son Yuri were still alive. While a small part of his mind wondered if it might be better to leave the American scientists to develop a cure on their own, orders were orders and he needed to follow his. It wasn't like the Admiral didn't know what he was doing and his father, who had retired a Captain, had always had good things to say about the Admiral's leadership. He would follow the Admiral's orders since he seemed to be the only one who really seemed to know what to do when the flu came and the politicians started dying off. The Admiral seemed to have a plan and that needed to be followed through.

It was nearly time.

Lieutenant Kara Foster was just sipping her coffee in Nathan James' CIC when the contacts appeared on her screen. She'd been watching the two green dots, wondering what Danny and Frankie were up to. Probably goofing off. She thought. Little did she know that quite soon she would regret that thought.

She wasn't quite sure what to think about Lieutenant Daniel Green. Not so much about Lt Green. More about her relationship with him. That, in itself, was the problem because she was a lieutenant in the US Navy and she shouldn't be having a relationship with another officer on the same ship. She didn't know quite how it happened. It had never been an issue before. She prided herself on being professional and she had been. And then Danny came along with his cheeky smiles and sexy butt. But it wasn't just that. He was caring and gentle with her as well and she didn't think he was the type to have a fling on every ship he was on. She knew that she really had started to care for Danny and that she hoped it lasted, but all the time she worried about being discovered and losing everything she had worked for.

But she had to clear her thoughts quite rapidly as first two red dots and then two more appeared on the radar screen. "What the-?" she choked out as Mason called, "Aircraft! Position seven six decimal three five north zero five nine decimal five eight zero!" Then it all started to go wrong.

Lieutenant Danny Green looked up rapidly. Is that a helo? he thought as Frankie looked up next to him.

"Those aren't ours man." Observed Frankie as four helicopters flew towards them.

"No shit!" observed Danny, recognising the Russian Mil attack helicopters, "They're Russian!" The two Navy SEALs sprang into action, jumping on their snowmobiles and gunning them towards the scientists' position as they co-ordinated the anti-air with Smith and Berchem over their radios. He didn't even have time to think about where Halsey had gotten himself to.

"Shit!" gasped Danny as the Russian helo fired rockets at them, neatly bisecting him and Frankie. They took evasive action as they led the chopper towards the ridge, right into the path of Smith and Berchem who blew the chopper out of the air with a SAM. But there was still one more chopper, and as Smith turned around to steer back towards the scientists, it nailed their snowmobile with a rocket.

"No!" screamed Danny, but he had a mission and he had to focus on saving the scientists. Putting his concerns for his men to the back of his mind, he followed Frankie towards the position the scientists were working from.

As they drew in, the other chopper was circling. Obviously out of rockets, a gunner was strafing the scientists with a large calibre machine gun. The two SEALs jumped off their vehicles and started hosing the chopper down with their own guns. Bullet holes pock marked the fuselage and it spiralled into the ground and blew up. But the damage had already been done. While he could see Tophet on his feet, Dr Rachel Scott, erstwhile leader of the scientific mission was lying in the snow, with her legs surrounded by a halo of red snow.

"Frankie, get Tophet and go!" he screamed into his mike, "I'll get the Icebitch!"

"Yo Danny," replied his partner, "already on my way." He motioned to the man, "Come on Doc," The scientist didn't need to be told twice and clambered on. Frankie got on in front, gunned the engine and drove off, Tophet holding onto him for dear life. All the time Danny guarded the group, looking out for further threats.

He knelt down next to Dr Scott. "Where are you hit Doc?" he asked her.

"Leg," she gasped, "it's not serious." She added, "we need to get my samples." While she was a pain in the ass, Danny had to admire someone as mission-focused as that. He picked her up in his arms and gently put her down on the back of the snowmobile, then he picked up her box and gave it to her.

"OK Doc," he told her, "hold onto my waist and we'll get you back." Then he took one more look around the horizon, got on the snowmobile and started to follow Frankie.

Out at sea there were two large explosions and then two more. He heard the rapid-fire guns aboard Nathan James open up followed by an explosion, and then the crack of the five-inch, followed by another big explosion. Shit, they hit Nathan James as well. He hoped Kara was OK. She should be, buried in the depths of the ship in CIC. But now he needed to focus on his job.

"On the way Frankie," he called.

"OK man," replied his friend, "just one more ridg- SHIT! Enemy in-" Frankie was cut off and an explosion lit up the sky in front of him. As he crested the ridge, he saw Frankie's snowmobile on its side next to a big hole in the ground. Two bodies lay beside it. A black-clad figure was running towards the bodies but stopped and turned towards him. He gunned the engine, hoping to put off any targeting, and drove on past the wrecked snowmobile. Tophet had taken the brunt of the explosion and was blown in two. Frankie's arm was lying some distance from his body and he wasn't moving.

"You better be fucking worth it," he grunted to the Icebitch as he drove away, likely leaving his friend to die. As they slowed to crest the next ridge another black-clad figure appeared in front of them. As Danny turned to take evasive action an RPG exploded next to the snowmobile, blowing it in the air. Danny rolled over and came up firing, taking out the enemy soldier, but he got a shot in as well, hitting Danny's right arm. Danny rolled up, taking in the scene.

He couldn't see any other targets, but Scott was lying on the ground trapped by the snowmobile. She didn't seem to be in any worse shape but couldn't get out. She was still holding onto her samples, he noticed. He ran back to the vehicle, tying a tourniquet on his arm as he did so.

"Doctor, can you get out?" he questioned, keeping his gun out, one eye on her and one eye around them. He tried to shift the Snowmobile off her, but it was jammed fast and he didn't have the power with his arm injured.

"No," she said quietly. "Lieutenant Green, I know you don't like me, but I have to ask you to trust me and to do something you're really not going to like. I have to ask you to leave me here and make sure the samples get back to the ship."

"No way," he told her, "you're my mission. You're why my men are dead."

"You're wrong," she told him, looking him in the eye. "These samples are your mission. I kid you not. They could make the difference between life and death for a lot of people." His gaze sharpened on her. "I'm sure you don't think that unknown soldiers attack every bird-watching mission to the Arctic do you?"

"They're Russian, Ma'am," he told her.

"It doesn't really matter who they are Lieutenant. Will you obey my order?" she asked.

"Ma'am…"

"Look leftenant," she said, enunciating carefully, with her British accent getting the full "lef" out of the lieutenant, "let's be brutally honest here. I'm trapped and may not get out of here. There are still more enemies out there and, even if you do get me out, I'm an injured civilian and you're a highly-trained special forces soldier who can hide away or stay alive in difficult conditions and who can move a lot faster than me. Obviously, there's something wrong with the ship since they haven't contacted you or sent the helicopter to get us out which means that we might need to survive on our own for some time without support. These samples MUST get back to Nathan James. I'm not lying to you when I say the survival of the world may depend on it. I will slow you down and increase the risks of us getting caught. Now. Will you follow my order?"

He looked at her with new respect. It was clear that she believed in what she was doing and was willing to sacrifice her life for that. He made a decision.

"Yes Ma'am, I will."

She gave a tight smile. "Thank you, lieutenant. You'll understand when you get back to the ship, I'm sure. Now, time is short. Please tell the Captain that I'm carrying sealed orders from the Pentagon in the safe in my stateroom." What? Did he just hear that right? She smiled at this reaction. "The code is my birthday, six digits," she paused, "And please tell the Captain I'm sorry he had to find out this way. I'm sorry you had to find out this way as well, and I'm sorry about your men, but you'll understand when you find out why. Now please, GO. And take my samples with you," she finished firmly, looking directly at him. There was sadness and empathy in her eyes. Something he had never seen before from her. Normally she was very formal with them.

"OK Ma'am," he replied, "good luck."

"You make it sound like goodbye," she replied with a half smile. "Just to make sure, when I get back to the ship, I'll be needing a tea, preferably by intravenous drip! It's in the box on the right-hand side of my desk in the lab," she told him.

He was grateful for her attempt to reassure him. He gripped her shoulder briefly with his left hand, hefted his rifle with his right hand (despite the pain), clipped her sample box to his belt and set off. He kept an eye on her position until he crossed the next ridge but didn't see anyone else. Now to disappear, he thought. He kept all of his concerns about Halsey, Frankie and the rest of his team out of his mind. He would grieve for them later, now he had to focus on the mission.

"Shit shit shit!" Captain Tom Chandler cursed up a storm. They had successfully destroyed the two enemy choppers (they had looked Russian but he couldn't be sure that they actually were) that had come for his ship but they'd taken some damage, with by far the most severe and mission-limiting being the damage to the helo bay door which meant it would be another hour before they could launch the helo to look for their ground teams. Short range communications had also gone out for about an hour due to a damaged line, but they were up again now.

But the problem was that the ground teams weren't transmitting, and he couldn't see them on radar. He had dispatched boat teams, but they were still 30 minutes out from the target area. And then it had got worse. About forty minutes ago, just over an hour after the initial attack, another airborne contact, obviously another helicopter, had come in, circled for 10 minutes, landed, then left. It seemed that the enemy had got what they wanted, and Tom Chandler had no idea what that was.

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A/N 1 Dates are going to be really important in this fic. Thanks to Jules06 for pointing out the horrendous typo in the first version I uploaded. I've assumed that season 1 is set in 2014 and season 2 in 2015. I assume that episode 1 kicks off in May 2014, with the Russian attack around the beginning of October, arriving in Florida around 25 October 2014 and they arrive in Cuba around 26-27 October and get to Baltimore around the end of December 2014. I would expect they get to Norfolk towards the end of the first week of January. Dates are going to be very different in my version but I wanted to explain where I'm coming from.

A/N 2 So if all goes to plan (and we all know no plan survives contact with the enemy!) this fic should have about 25 chapters, of which about half are already written/planned. Fair warning, there are elements of this story that include quite disturbing scenes with mature (adult) content. If you don't like those sorts of stories, then this may not be the fic for you.

A/N 3 Bold text is dialogue directly quoted from The Last Ship episode, Phase Six.