Thank you so much to all my reviewers. Your comments are always valued and appreciated. So, here's the next stage. There be some whump here and more. Bits are a little dark and some may be distressing. Much of this chapter is based on personal experience, either directly or anecdotally and some I found quite difficult to write.

The mood in the jumper bay was sombre and anxious, though in other circumstances the two waiting figures with matching slings might have been comical. Richard Woolsey's pale and shiny countenance told of the pain he was still suffering from his broken collar bone but the nursing staff had been unable to obey Jennifer Keller's orders to keep him in the infirmary at all costs. He'd not really had time to catch up on the events of the past few days either, but both he and Lorne were determined to stand and wait for their military commander; whether it was to pay last respects or greet him back alive was yet to be seen. The last and hurried message from the rescue jumper had been that they were fighting to keep him alive but that it didn't look good, but nothing on why or how he was so badly injured.

As the familiar sound of the gate activating rumbled up through the floor to the jumper bay, Major Evan Lorne said a silent prayer. After all these years and battles won and lost for the city, John Sheppard did not deserve to die on an off world holiday with his wife. From the beginning, he'd not been one of the Sheppard detractors and his loyalty had been unwavering since; he'd never labelled the man's bravery and self-sacrifice as foolhardy or reckless, unlike some of the more senior commanders at Stargate Command, and had fought a constant battle to alter the entrenched opinions of younger soldiers arriving in the city who, even after all these years, still believed some of the unkinder rumour mongers. So, it was with a sharp intake of breath that he waited for the jumper to settle in the bay.

Inside the jumper there was silence apart from the sound of Jennifer Keller trying to resuscitate John. Cat was being attended to by one of her nurses. In other circumstances, she would have had Jennifer's full attention, but she hadn't been able to pause since the rescue. How his body was still trying to stay alive she couldn't say and she hadn't been able to have a look yet at the wound behind the bandage on his head. The craft landed with a little bump and almost before the back hatch was open, her medics were on board, with gentle urgency picking up the stretcher and placing it on the waiting gurney and then speeding off down the corridor to the nearest transporter, with Dr Keller still desperately trying to keep him alive, and his close friends not far behind. Following, was the gurney with Cat on board, unconscious through exhaustion and dehydration rather than anything else, a drip already giving her the fluid she badly needed. And left in the jumper bay were the two men. Lorne looked at Woolsey for silent permission which was greeted with a nod of the head, and then he too ran after his commander and friend.

Richard Woolsey sighed before heading back down the stairs to the gate room and his office. He would take his mind of things by finding out everything that had happened in his 'absence'.

She was in a boat on choppy waters. Something was wrong but she didn't know what. Someone should be with her in the boat but she didn't know who, but her rising panic suggested something bad had happened. She could swear that she had just heard a plop as though something or someone had fallen into the water. Jumping up, the boat rocking precariously under her, she looked over the edge into the water. Far below was a familiar form, rising slowly upwards towards her and the surface. As it appeared through the murk, she recognised John. His mouth was open in a ghastly gape for air and his eyes were cloudy and dull. She tried to grab him but he was just too far away beneath the water. Suddenly, his body twitched and he grasped her hand and she heard a distant voice shout 'help me!'

Cat screamed. She felt firm hands holding her and heard quiet voices soothing her and as she became more conscious she stopped fighting them. Blearily, she saw Teyla and Ronon, one on either side of her, comforting and soothing her. Familiar smells permeated her senses: antiseptic, metallic, chemical. The blue-green walls shone mutely, reflecting the dulled lights of the infirmary. Reality hit her hard as she began to come too.

'John?' she asked tentatively, then shut her eyes in preparation for the inevitable.

Teyla glanced at Ronon. 'We do not know, Cat. He has been in the operating theatre for several hours and we have heard no news. John always says that no news is good news, so I think that we must stay hopeful.'

Cat registered for the first time how tired her two friends looked and took a deep breath, desperate for something to take her mind of what might be happening in the next room. 'Tell me? What happened here? All we knew was that something was wrong then there was some kind of explosion and nothing worked any more. We had to leave the jumper behind. John...,' here she paused and regained her composure, 'John tried to get it working but it went dead and we had to walk across land to find Carson's boat.'

From the look on her face, Teyla could tell that there was much, much more to tell and she was burning to find out, but now wasn't the right time, not with her old friend's life in the balance.

'Rodney discovered that someone had sabotaged the city's systems, but it was too late. There was a series of explosions around the city and everything went down. Then, The Genii arrived through the gate and took the city.' Cat's eyes widened. Memories of her own treatment and torture under The Genii still painfully fresh in her mind. 'Rodney managed to get some of the systems back on line and we fought them off. He sent an energy burst through the city's corridors.' The similarity with how another Genii incursion had been foiled hadn't escaped any of them. 'Many Genii soldiers were killed in the burst, although some still managed to escape through the gate.' Again she paused, and this time Cat caught a sense of something unsaid.

'What aren't you telling me, Teyla? Is everyone alright? Oh my God, how's Mona? Is she alright?' A vision of losing both her loved ones crashed over her like a tidal wave.

'Mona is well. She is sleeping now, but I am certain she will want to see you as soon as she wakes up.' Then Teyla told Cat about Janet and how she had died saving her and the children. And of how Mona had helped Rodney activate the Ancient systems. And of the odd conversation overheard by Richard Woolsey in the gate room: that The Genii's purpose had been more than just sabotage or revenge; they had wanted something and had clearly found it, though nobody had yet been able to discover what.

It was a lot to take in, but it had, at least temporarily, distracted them from their most pressing worry so that almost unheard Jennifer Keller entered the room. She looked exhausted and Cat held her breath for the news that she was certain was coming.

'Well, we have stabilised John for now,' she said. 'It was touch and go for a while, but he is out of immediate danger.' Jennifer paused. The doctor's role suggested that she should lay the facts objectively in front of the relatives, but these people were also her friends. 'He has a serious head injury. The bullet had lodged in his left temporal lobe and has caused some damage. Fortunately, it wasn't too deep and we have managed to remove it. There is some swelling of the brain caused by the shock of the bullet entering the skull and we have put in a small shunt to relieve the pressure and allow the brain to settle down and recover. He is lucky. There is no evidence of a haematoma at this stage. However, he has contracted a nasty infection and has a very high temperature. As well, he was severely dehydrated.' Doctor Keller inwardly winced at the look on Cat Sheppard's face but knew that she needed the whole truth. 'He is in a medically induced coma at present, although he hasn't been conscious at all. The brain needs time to recover a little. We also have him on a strong dose of antibiotics to try to ward off the infection. You can see him if you want, once we have him properly settled in ICU, but not for long. You need to recover too, you know.'

Cat's brain was racing. She needed some answers: something definite. 'But he will be alright, won't he?' she asked.

Jennifer looked from Ronon to Teyla, then back to Cat. 'We will have to wait. Brain injuries react in different ways. But, you have to understand that he is critical at the moment.'

Painfully, Cat got herself out of bed and dressed, against the advice of the ministering angels who tried to make her rest more. She knew what to expect in ICU but it was still a shock to see him pinned out on the bed. Tubes entered his body delivering necessary fluids and exited it doing the same and the machines bleeped and flashed around him. Somehow, she'd expected to see more of his face, but his head was even more bandaged now. Behind his one visible eyelid she could see the movement of his eye as it twitched to whatever wild or banal dreams he was having, but beyond that he was stiller than still, the only other movement being of his chest as the ventilator blew life-giving air into his lungs. She knew that a nurse would be with him twenty four hours a day as he struggled to recover but needed to be with him too and gratefully took the chair offered to her. From here, she could stroke his arm, soothing him when his head pressures peaked or when other unknown alarms bleeped or soared, as they did with frightening frequency. Behind her, the tall figure of the Satedan hovered uncertainly, uncomfortable in such distress but unwilling to leave the man he considered to be his brother; and Teyla placed a soothing hand on her shoulder; at the back of the ward stood the stoic figure of John's second in command.

Suddenly, there was a commotion in the other room and the sound of shouting and screaming. A struggle was clearly taking place, then the door swished open and a mini-whirlwind blew into the ward, followed by a very out of breath Rodney and Katie McKay.

'Mama!' shouted Mona, 'where's dada?' Cat nodded to the McKays to let her daughter come in unhindered, holding out her arms. The little girl rushed to her and leapt onto her lap, clinging and sobbing into Cat's neck but as the tears subsided, she noticed the prone figure of her father lying on the bed. Mona was rarely silent, but the sight seemed to mute her completely and her eyes opened in shock. With one long frightened stare she looked in his direction before turning on her heals and, back straight and firm, walked from the room, grasping Katie McKay's hand firmly as she did. Katie looked back to Cat for permission but all Cat could do was shrug her shoulders and allow her daughter to leave. It would be some time before Mona would be prepared to visit her father again.

Over the next few days, the little group found themselves a rhythm and routine which was surprisingly comfortable given the circumstances. If Cat had allowed herself to think about it, she would have understood what the medical staff knew all too well: that families need to find something 'normal' to hold onto even in the direst and most stressful circumstances. They took it in turns to sit with John and every hour the shift would change, allowing each to rest or eat, even talk and laugh at times about nothing and everything. And nothing changed apart from a few mini crises. Every day, the nurses reduced John's sedative in order to test his alertness and every day he stayed motionless and unresponsive. They assured her that this was normal and she tried to believe them. Every day, Cat woke after a night of exhausted sleep to a gnawing panic in her gut and ran to the infirmary, dreading what she might find there. It wasn't until the fifth day that something changed.

As she approached the infirmary, Cat could hear something happening: the sound of a scuffle or fight and shouting, both male and female voices, but the door to the little ICU room was firmly locked. The noises were definitely coming from within. It was only seconds, but it seemed like hours before the door opened and a rather ruffled male nurse exited. Seeing her there, he attempted to straighten his uniform and appeared to take a deep breath.

'Um..Doctor Sheppard,' he muttered. 'I think you might say that Colonel Sheppard has just shown the first signs of being more conscious!'

Jennifer Keller emerged behind him. 'Alan,' she said to the young nurse,' go and get yourself cleaned up and have a rest. We can manage from here,' and she smiled affirmingly at him, before turning to Cat.

'Well!' she said. 'I think you might say that your husband is showing some of his fighting spirit! We reduced his sedation this morning and he certainly woke up. The trouble is that he wanted to get out of bed and started fighting with the nurses. It took four of us to hold him down and stop him pulling out all of his tubes and his head pressures began to spike rather dramatically. I don't think it's quite time for him to come round properly yet and we've put him back under a different sedation. Next time, he should come round more gradually. But, I think you might say that this is a very hopeful sign, Cat.'

Over the next few days, there were similar moments of chaos but gradually the battles lessened. A couple of times, Cat was certain that John was about to come to, his one visible eye open revealing a bloodshot and unfocussed eye, and she was certain that he squeezed her finger gently once or twice. But still, he remained resolutely unconscious. It wasn't until the tenth day that something happened. She had just left for a rest and Ronon had taken over the shift when she heard heavy footsteps running down the corridor after her and a loud voice shout, 'Cat? I think you should come back to the ICU now. John needs you.'

With trepidation she looked up at Ronon then together they ran back to the little room. Beginning to stir was John, his visible eye more obviously open and he seemed to be looking around for something. She rushed to his side and took his hand.

'Sweetheart? John? Can you hear me? It's me, Cat,' and she stroked his arm gently. The eye turned towards her and she could see how difficult he was finding it to focus on her, then he simply mouthed her name and tried to smile. She'd stayed so strong for so long that his smile released what last resistance she had and she simply put her head on his chest and cried, tears of relief and exhaustion. When she looked up, he was asleep again, but this time Jennifer assured her was proper rest and not just drug induced.

'I must go and tell Mona,' Cat eventually managed to say. 'Perhaps now she'll come and visit her dada.'

The residents of Atlantis greeted the news with tempered joy. Too many of them had experienced the death or injury of loved ones while in the city and they all knew that Colonel Sheppard had a long way to go before he was fully recovered. No-one openly spoke of the possibility of brain damage or of less than full recovery.

Richard Woolsey was bent over some paperwork in his office when Ronon, Teyla, Rodney and Lorne entered. He'd called a meeting as soon as he heard the news about John. Over the past days he'd managed to piece together most of what had happened but he needed their individual reports of, what he had named in his paperwork, 'The Atlantis Incident'. The 'what' had happened was fairly clear, but they now needed to resolve the 'why'. And for that, he also needed Catherine Sheppard's report of events on the mainland. In turn, the group told of events from their perspective. The death of friends, especially Janet Donaldson, hung heavily over them. There were still funerals to arrange and messages to compose to loved ones. Normally, John took full responsibility for such missives to members of the military contingent, but Lorne would have to do it this time and he was less than comfortable with the charge. They decided that he and Woolsey would write the messages together. Who knew when or if Colonel Sheppard would be able to take that unfortunate task again?

'So, let's summarise what we know so far? It began with sabotage of minor systems by someone who had either infiltrated the city or was already here. We have performed a full register of current inhabitants and there are several possibilities. Unfortunately, we still have three missing persons and we must assume that our saboteur is one of these. It may be that Doctor Sheppard can be of some help in this matter and she will be joining us shortly.' He stopped and raised an eyebrow at the team opposite in an attempt to forestall the expected objections to this. 'It is necessary that we have all the information. I, too, am sorry to bring her into this at this time.' He paused briefly then continued. 'This person must have had the Ancient gene and some good engineering knowledge. The resulting explosions caused our systems to go off line and allowed The Genii to gate in and take the city. Thankfully, due to the bravery and determination of many and, of course, Doctors McKay and Zelenka, we managed to retake the city. However, something has been taken from here that The Genii wanted and we must assume that this was their main reason for the attack and the damage was a gratuitous side-effect. It is imperative that we find out what this 'something' is, which could be easier said than done, especially if, as seems likely, it is some kind of artefact from the Archives. Without a current Archivist and with the damage down there, finding what it is could prove almost impossible.'

He paused again at the sound of footsteps across the walkway to his office. Cat walked in tentatively. She knew that she would have to recount the details of what happened on the mainland sometime, but also that it would prove painful to do so, especially since she blamed herself for much of what had happened. Had she treated Dane with more respect, said a proper farewell and thanked him for all he had done for her, then maybe, just maybe, none of this might have happened.

'Thank you for coming, Doctor Sheppard. I know this won't be easy for you, but could you please give an account of what happened on the mainland?' He attempted a reassuring smile.

And so she did. She told them everything she could remember, trying to avoid their faces, knowing that some of it would cause John's friends distress or anger and she didn't want to see pity for her there either if she were to remain strong.

'Thank you, Catherine,' Woolsey said. 'That has been a great help. At least we now know that our saboteur is dead. Unfortunately, it also means that one of our missing three is also dead. It would seem that this 'Dane' fell right into the hands of The Genii and they used him to their own ends, as always. I think that we should focus all our efforts now in finding out what they stole, don't you?

'Once things have settled down a little with John, I might be able to help there,' offered Cat, slightly unwillingly. The thought of going to the place where Janet was killed was not a pleasant one, but after what she'd been through over the past two weeks, certainly not the worst thing she'd had to face. 'I know she made some changes to the cataloguing system but it is still basically what I set up. I can try to find out if anything is missing?'

'You will need some help, Catherine,' answered Woolsey. 'It's a mess down there. Lorne? Please detail a couple of men to help when Doctor Sheppard is ready? Thank you.' And with that, he put his pen down neatly next to the writing pad, which he closed firmly. A sign, they all knew, that the meeting was over.

Why was it that sometimes she could walk to the infirmary with a spring in her step and other times she just had a feeling that something was wrong? Today it was the latter and the feeling was very powerful. In truth, she was rarely right, but it didn't stop the panic rising. John was now out of intensive care and in a side ward in the main infirmary. The antibiotics had begun to manage the infection but in other ways the progress was painfully slow. Sometimes, he'd seem quite alert and lucid and then he'd say something that made her realise just how far he had to go. The ventilator tube had come out immediately he was conscious and he was now breathing for himself, his voice less hoarse now from the inevitable bruising it had caused. Yesterday, for example, he'd claimed all day that he was going home that evening; that he was much better and that no-one else knew what they were talking about. Jennifer had told her that it was perfectly normal where there has been a brain injury, but that didn't help. And on top of this, Mona was resolutely refusing to see him. All she had said since that day in ICU was that he wasn't her dada at the moment and that she didn't want to see him until he was. Cat tended to sympathise. She'd been so angry with him, or at him, or for him, she didn't know which, that she'd had to leave the infirmary just to calm down.

He was asleep when she arrived and she gasped at how normal he looked today. Sometime overnight the large bandage had been removed and there was a padded plaster covering the wound. There would be a shaved patch under there too which he wouldn't be happy about. His dark hair was still matted and flat, though someone had clearly made an attempt to clean away what was left of the blood and dirt and, more importantly, both eyes were visible. The nurses had also helped him to shave and in sleep, though very thin and drawn, he looked closer to his old self. She sat down on the padded chair next to the bed, the place that had become an almost permanent residence for her, and rested her chin in her hands, taking in the familiar shape of her husband. It seemed like an eternity since he'd held her in his arms and told her he loved her and she longed for that warmth and security.

She must have drifted off to sleep because when she woke up he was sitting bolt upright in bed, staring at her wide-eyed, his pupils dark and large, made even more so by the thinness of his face.

'John?' she started, 'How are you feeling...?'

He leered back at her. 'I'm fine, gorgeous. Why don't you come here and I'll show you exactly how fine I am.' At this, he whipped off the bedclothes, his erection clearly showing how 'fine' he was. 'Come and sit on this,' he said lustfully as he tried to grab her. As he leant forward, he lost his balance and toppled off the edge of the bed, landing with a hard thump on the floor. Cat shouted and the nurses came running, quickly picking him up, settling him back down and checking him over for any injury. As they did, his hands roved over them, clutching at intimate parts of their bodies. With horror and tears running down her face, she ran from the room, straight into the small form of Jennifer Keller, nearly sending them both toppling over.

'What's the matter, Cat,' asked Jennifer quietly. 'Come and sit down. Over here.' She guided Cat to her small office. Through half-controlled sobs, Cat explained what had just happened.

'I am so sorry, Cat. I should have warned you that this was a possibility. Some head injury patients suffer from increased sexual behaviour and it can be totally random and uncontrolled. I once treated a vicar who insisted on showing himself to all the nurses. You must understand, it isn't really John and it will settle down as he recovers more. In some ways, it's a good sign.' Cat gave her a look that said 'are you mad'? 'His recovery is following the usual protocols. You have to stay positive, for his sake, Cat. We will just have to wait until it passes. In the meantime, I rather suspect that a few nurses who have been lusting after your husband, might be ready to volunteer for extra duties!!'

Cat looked at her, horrified at the vision of sex-starved nurses taking advantage of his weakened condition before Jennifer recognised the effect of her joke and apologised. 'Sorry, bad joke. All my nurses are consummate professionals.'

It was hard to smile, but Cat allowed herself a small one at Jennifer's terrible medical humour. 'So, if this is normal, does this mean he's going to be alright? That he will be back to his old self soon?'

Once again, Jennifer was torn between doctor and friend. 'I am sorry but I can't promise you that. It is entirely possible that he will be permanently changed due to the injury. You may have to get to know a whole new John Sheppard, or at least a slightly different version of him, or he may be unaffected. There is now way we can predict what will happen.'

Cat shut her eyes in an attempt to shut out the distress she felt then seemed to make a decision. 'Well, if that's the case, it was fun getting to know John Sheppard the first time round. Let's hope the second time will be even better!' and she smiled a determined smile at her friend, before turning her back resolutely (just like your daughter, thought Jennifer) and walked back firmly to his room, ready for the next challenge.

As always, please R&R if you want. I always appreciate the encouragement. This was not an easy chapter to write and I'm looking forward to some TLC and recovery scenes – and that East Pier scene as well.

Mind you, there is a way to go and some mysteries to unravel – whether wholly or partly you will have to wait and see!!