Disclaimer : The characters and genre used belong to the appropriate owners I hold no right or ownership to their work.

Author's note: hey guys sorry for the delay life is a bit hectic right now . Thanks again to everyone who has taken the time to read and review my story. I will definitely take all your suggestions on board and hope to improve quickly.

* = John talking to Atlantis in his mind

"= regular people talking to each other

References made to the SGA book Reliquary and the book mirror mirror

"Colonel " greeted Major Evan Lorne as John walked into their shared office , with a quick nod he returned to his paper work hoping to get all of it down before the day was finished .

"Major how's it going , what did the doc say about your leg ?" John gave him a searching look as he sat down and booted up his own computer . Concern for his second in command clear , after all having a puddle jumper dropped on your leg during a Wraith attack isn't something you just shake of quickly .

" Dr Beckett says I'm on the mend and should be able to return to active duty in about 2 weeks as long as I don't strain myself ". The relief in his voice was evident , Evan loved his job and would hate to have been sent back to earth with a medical discharge , although privately he was pretty sure the colonel would do everything to keep him even if it was as a civilian contractor and not a member of the air force.

" That's great news Evan, things are going to start changing around here and I'm going to need my best officer by my side to get things done right." Looking straight at the Major, John tried to convey how serious he was .

Evans fingers stilled as he stopped what he was doing , suddenly fully alert paying close attention to what his boss was about to say.

John smiled seeing the Major shift his full attention to him . After years of working together the two of them had developed a short hand where verbal communication was rarely needed , each being able too anticipate the others needs without being asked. It was that close bond that made John realise how lucky he was to have Evan assigned as his second in command , especially when he could have ended up with some of the more dogmatic militant officers .

John proceed to spend the next half hour explaining all that has happened and what his plans going forward are and how it will affect the expedition going forward.

" As I've said things will be changing and not all those changes would be approved by the IOA or even the top brass , so I have to know Evan if you are on board with this? Just know that whatever you decide I will respect your decision and it wont change how I view you. You have earnt my trust and friendship so if you decide you can't follow me down this road I won't hold it against you and I will try my best to make sure it won't effect your career in any way".

Evan as always took the time to think things through properly before making a decision. Had he been asked this before joining the Stargate program he wouldn't have hesitated to blow the whistle and report this to his superiors. However after years working at the SGC then later being assigned to Atlantis he has learnt that those in charge often fail to see the bigger picture and focus more on the politics. Experience has shown him that ignoring the advice of those who are actually in the thick of a situation has never produced good results and has in fact has cost lives of good people which has lead him to become rather disillusioned with those in charge.

"John I would love to say that I'm 100% loyal to the brass but after all we have been through and knowing the fight it took to get the city back to Pegasus when those in charge would have abandoned this galaxy to the Wraith causes me doubt the worth of such loyalty . Knowing what they would do to you and Atlantis if they knew the truth... I cant standby and let that happen . It's not often that men like us get to fight for a truly just cause. So Lieutenant Colonel John Sheppard, my friend, you will continue to have my full support and backing".

It took John a second to swallow the lump in his throat overwhelmed by the support Evan was showing.

As a military man he was well aware of what Evans support truly meant and just what he was willing to risk by giving him such support. To know that he had the trust and respect of such an upstanding officer meant more than words could say.

"It truly is no surprise John , that the people around you would lay down there lives for you . You give so much of yourself to your people it inspires great loyalty in those you meet . I really have been blessed with such an honourable Guardian".

*thanks Atlantis in not sure I deserve it but I will try to hold myself to that standard *.

" Thank you Major Lorne for your continued support . Now that your on board I have some jobs I need you to see to. First I am suspending all none essential gate travel, for too long we have ignored the city itself so until further notice all gate teams will be assisting with the repairs and exploration of the city so can you see to it that they're assigned to Zelenka's teams as and when there needed . Second I want you to order a full inventory of all our supplies and equipment, I want a full accounting of what we have and what we need so we can start getting a surplus stock whilst earth is still willing to provide it. I'm hoping that once Rodney gets the Asgard systems online we will be able to synthesize all the equipment that we could need.

Finally I want you to go through all our mission reports where we have lost or encountered a puddle jumper. Atlantis was built to hold 50 jumpers spread across a number bays throughout the city, according to Atlantis we currently have 21 in various conditions . I know we've lost or wrecked some and the ancients lost a few as well so the more we can salvage the less we will have to try replace later down the road when we have the capacity to make more".

"Okay I will start up a duty roster with the new assignments in mind and see to it that the inventory is done before the next dial out to earth so we can make the supply request. As for the jumpers do you want me to send out teams to get the ones we can salvage or should I hold off till later? ".

Asked Evan , already planning out the changes that were about to take place across the city . Feeling quite excited about the coming future especially having a few ships at their disposed secretly hoping he would be assigned one of the ancient ships again, remembering how cool it was to pilot the Orion before it was lost in the battle against the wraith.

" For now you should just make a list of which ones we can retrieve. For the time being the majority of our resources and man power will focused on fixing the Sun Tzu , Tria and Atlantis . Once we have at least one of the ships repaired we can go over the list you put together and start the salvage process" .

After a few more minutes talking they both spent the next few hours going over all the paperwork that comes alongside running the programme before calling it a day with Evan retiring for night and John making his way to the control chair for his next lesson with Atlantis.

Chair Room

John had spent the last hour just immersing himself in the city's systems getting a feel for what was working and where all the different repairs needed to be made with Atlantis providing guidance and information.

Already seeing where Zelenka had started the repairs on the collectors and how Dr Parish and his team of botanists have begun cleaning out the advance hydroponics bays. As he began to call it a night and pull himself out of the interface he felt Atlantis grab his attention again .

"John before you retire for the night there is one final thing I would like you to start working on. As I have previously stated there is more to being the Guardian than just a stronger connection to my systems, there is also a physical difference as well . Today I would like to start building on those physical changes."

* Okay I was wondering about that , you never really explained what changes will be happening. It won't be anything dangerous will it?*. Asked John cautiously.

After being turned into a bug and seeing Rodney almost die because of the ascension device he had gained a healthy fear of things that can change your physiology.

" Be at ease John for the changes that will happen will come naturally and at a pace that your body can handle with little side effects . As you know the Alteran people as they evolved gained many different abilities . Such as improved health, strength, healing and telekinesis just to name a few. As the Guardian you will gain many of these abilities over time with varying degrees of strength something that would've happened with or without you coming to my city. What I would like to start today is to help you begin learning to control and grow these powers that you always had the potential to use".

* So are you really saying that even if I hadn't joined the expedition I would've gained these powers? *.

To say John was shocked would be putting it lightly, having read all the reports on those that had gained powers and having experienced it first hand he knew that it only happens to those that are more evolved like the Ancients or those that were enhanced like Rodney and the Ori Priors. To know that he was one of those who naturally had the potential for these abilities made him question just how human he really was.

"Yes, when you first arrived here you were on a genetic standard more closely linked to the Alteran then you was human as is the case of many of the strong gene carriers . It is part of the Alteran genetic make up that all those with the ATA gene are drawn to each other as a way to ensure survival of the species. If you like at a later date I can do a full genetic screening for you, I would not be surprised if at least 70% of your ancestors carried the ATA gene in one form or another given how strong your ATA gene is. As to the development of any abilities you would have gained, they would have grow at a much slower rate without direct contact with Alteran technology, however you already have benefited from your advance ATA gene. It's no coincidence that those with a strong ATA gene excel in their chosen field such as your ability to pilot any craft you sit in and you skill with numbers or Dr Beckett's easy grasp of medical and genetic science and Dr Kusanagi's understanding of advanced physics."

John sat quietly for a few minutes still reeling over what Atlantis has just told him , and the more he thought about it the more it made sense, when he considered himself and all the other strong gene carriers that he knew they all were the top of their fields of study ,even his brother Dave and their dad were both great business men who could turn any project into a profit no matter how unlikely.

Thinking about his dad made him seriously consider Atlantis' offer to look into his family especially having met a few ancients who look a bit like him Ikaros coming to mind, as they could have passed for brothers with how much they looked alike. The way Atlantis phrased it when describing his genetic state when he arrived almost made it sound as if it's no longer the same as it was before hand, instead of stewing over what she meant John asked her directly.

* I see what you mean I never thought of it that way but I guess it does make sense that some things do come easier to the ATA carriers then it does for others . But what did you mean when you said, "when I first arrived here," does that mean my genetics have changed? I know I turned into a bug but the doc changed me back right?*

" Since your arrival you have gone through many changes some small and others more profound. To begin with your interaction with my systems and other Alteran technology awoke and strengthened your dormant ATA gene. Your encounter with the Wraith especially the queen caused your bodies mental abilities to awaken and steadily grow. When you went through your minor transformation as a result of your encounter with Dorane you gained an increased sensitivity to my technology and more pronounced ATA response. After your transformation into - as you say a bug - Dr Beckett did return you to as close to your original state as possible however you do still posses Wraith markers in your DNA . Since that transformation your senses and reflexes are stronger as well as your natural healing abilities and mental powers.".

Atlantis paused for a moment to allow John to process all that she had told him before continuing, knowing that some of the changes she had already mentioned were times of significant trauma for him particularly his time as a bug.

" Also your experience within the sanctuary under the time dilation learning to ascend strengthened your natural core power, that alongside the ritual of sharing, you took part in with the ascended Alteran Chaya Sar, helped progress your development at an increased rate. If left on your own your abilities will continue to grow but you won't get the full benefit of them, with the proper training however I can teach you how to fully harness and control all of your abilitiets".

* I never realised that all those things had such an effect on me or that they were causing changes. Although I guess you could say that I find it easier to resist the Wraith with each encounter. From what you've described all of those abilities would be a great help and if they're developing regardless of what I do it makes sense that I learn how to use them properly. I'm not sure how I feel about not being classed as human or that I have Wraith DNA but I've learnt that there's no point fighting things that you can't change. So how does this work? What do I need to do to start controlling these powers?*

" Each of those encounters changed you in some way leading you to become the person you are today. More than Wraith, human or Alteran. I truly look forward to seeing you reach your full potential as you grow into your powers. First I will teach you how to connect to your core, the source of your powers. At first this will leave you feeling tired much like when you use the control for an extended period of time. But as you continue your training you will get stronger and begin to feel more energised. From there I will show you how to channel that power throughout your body and how to utilise it properly with your budding abilities. So John are you ready to start your training?"

John only hesitated for a moment taking a second to strengthen his resolve before conveying his readiness to take the next step in becoming the Guardian.

A/N: hope you all enjoyed , I tried to make it longer to make up for the late update . If anyone noticed any inconsistencies between my fic and the cannon either from the tv series or the books please let me know as I'm trying to keep it as close to cannon as I can . There will be a few things I will change either because in need it for the story of that I couldn't find exact info to use . Such as the number of jumpers in the city I couldn't find an accurate count anywhere so I'm guessing based on how big the city is there should be more then we see in the series . Rodney in season 1 compared Atlantis to Manhattan . According to Google Manhattan is 59.1 km² or 13.5 miles long so it makes sense to me that Atlantis is somewhere on that scale maybe a bit larger .