John gets orders to be transferred out of Atlantis and Rodney realizes the only way for him to stay is to become a civilian. Unfortunately, John may be smart but he doesn't have a PhD and is therefore unqualified to join the scientific staff. So, Rodney offers to marry him next time they're back on earth so that John can come back to Atlantis as his spouse. This has to start out with them being best friends and SLOWLY falling in love through a series of steps and trials. I would love to see Jeannie helping them plan the wedding and the varied reactions of their friends and colleagues.
Sheppard and McKay are doing reconnaissance on Wraith movements, and have taken a jumper through a Space Gate, but heading back, something goes terribly wrong, and the Stargate is destroyed. They're nowhere near another Stargate, Daedalus in back in the Milky Way, is weeks away from Pegasus, and even further away from them. There are no inhabitable planets in the system, so they set course for the next, in hopes of finding one, but they're alone. Even if they do find a habitable planet, they're still going to be alone together, and right now, in a very small jumper, with very little food.
McShep in the Terminator Universe
Texas born and raised John Sheppard, was raised to be Homophobic, and never exactly had a problem with that, after all, he loved girls, and nothing else interested him. Everything changes though when he meets Rodney McKay, someone that provokes his Homophobia, not necessarily because Rodney is Gay him, but because John is attracted to him.
An Ancient Device swaps Sheppard and McKay Consciousness', and it doesn't seem straightforward to swap them back. John hates being in Rodney's Body, feeling so unfit in comparison, and so out of shape, he's no match for Teyla when sparring, or Ronon when running, and starts pushing himself to get in shape, but falls foul of Rodney's Body's Hypoglycaemia, and Allergies. Rodney on the other hand is loving the change, he's fit, thin, and getting more than a little attention from people. He starts showing off the Body that John always underplayed, how strong it is, how effortless things are for him, and Rodney finds how much he likes Citrus. To John's he also rubbing it in; and Rodney is really getting on his nerves. He's jealous, he misses the attention, and he wants his Body back, but what's worse, is that he's actually a little attracted to himself.
Since his 'Ascension', McKay has changed in Sheppard's eyes, although no one else seems to have noticed, it's irking John, and he's becoming irate. Confronted, it was never Rodney, it was John; he was scared.
It's the 1800's, and John Sheppard is dying, he's contracted syphilis, and faces a terrible, and drawn out death. Despite his knowledge of science, his lover Rodney McKay can do nothing for him, but John is not willing to just give up. There is a Myth, that a cure for everything exists on the lost city of Atlantis, and with what time he has left, John searches for that city. Together, John and Rodney travel to Antarctica, where they discover the Stargate, and the way to reach Atlantis.
Separated from the rest of his Team, Sheppard is bested by a group of Wraith, and instead of being captured, or fed upon; he is brutally Raped by them. The others find him, but he doesn't tell them what happened, too ashamed to admit it. What's worse for Sheppard, is that he feels the need to do it again, to be taken that way again. Near desperate, he tries to find someone to do it, and he finds McKay, taking him to bed, and violently using him to satisfy a need, given to him by the Wraith. The more it happens, the more Rodney begins to care about John, but John doesn't associate Love with the act, it's just sex, riding Rodney, trying to take control, but still very much the victim. Rodney tries to change the nature of the 'Relationship' they have, to show John that the Sex doesn't need to be violent, that John doesn't need to be hurt, doesn't need to bleed, and doesn't need to feel ashamed. John's broken, tries to hide it with anger, and by lashing out, but he needs to break down, he's been hurt, and needs Rodney. And Rodney needs him, trying to make love to John and make this more than a continuation of the Rape.
Rodney McKay has never been able to handle his drink, something that he has managed to hide from everyone else on Atlantis, until getting particularly drunk one night, and have to have Sheppard help him back to his room. John has feelings for Rodney, and even though it could well be taking advantage of him, he feels that Rodney's giving out signals, and so makes a pass at him, something that Rodney doesn't reject. The next day however, Rodney doesn't remember anything, he never does, something John finds out all too clearly when he gets into Rodney's personal space, with an affection that shocks Rodney. Rodney genuinely doesn't have those feelings for John, and when he tells him as much, they're both left feeling awkward. John is agitated, and defensive, acting as though Rodney had been furious and disgusted, and told everyone what John had done, but Rodney hasn't, he wouldn't, and needs to clear the air. Rodney turns up at John's room, drunk, and all too easily, they sleep together, but Rodney was never drunk, and this time, remembers everything.
The entire base is exposed to an ancient device that turns everybody homosexual. It didn't effect John and Rodney who are already homosexual together, or Carson who is also gay. When they fix it, Lorne goes to Beckett saying that the anti-gay-ray didnt work on him and he's still gay. Carson proves to him that he's gay for real.
When Sheppard is relieved from duty, and suspended as military commander, albeit hopefully only temporarily, he has nothing else to do but spend time with his best friend. McKay can't keep calling him "Colonel", so starts calling him "John" instead, something that he has never done. You wouldn't have thought that something as insignificant as a Name would be so significant, but it is to them. The way that Rodney can't help but say it, the way that it sounds to John hearing it, and in the context of their friendship, changes things drastically between them. It's the final step their friendship can take before becoming something more. Even after John is reinstated, Rodney keeps calling him "John", and their relationship keeps spiralling into something more, but as subtly, and as unspoken as their entire friendship has been so far.
John Sheppard and Rodney McKay have been together for a while now, they're in Love, and it's on a well earned vacation back on Earth, that Rodney wants to take their relationship to the next level. Only Teyla, Ronon and Dr. Weir know about their relationship, and Rodney knows that because of the US Military, they can't exactly go public. They're taking their vacation in London, and it's on the London Eye, which is really just a big Ferris Wheel, something Rodney knows that John will love, that Rodney is going to Propose. If John accepts, then they'd be able to go through with a Civil Partnership before they head back to Atlantis, but is anything ever that straightforward?
John Sheppard's grandmother is dying, she raised John after his parents were killed, and they've always been very close, until last year, when their relationship was strained to breaking point, and when John met and married a woman that he purposed to love. John's grandmother saw this woman for what she was; she disliked her, and rightly so, because she knows, knows that she is not who John is meant to be with, and even refused to give her, her wedding ring. John is made to choose between his grandmother, and his wife, and it's the hardest thing that he's ever had to do, but he chose his wife, who then prevented him from even visiting his grandmother, until it was too late. John's grandmother was a wealthy woman, and John is the only beneficiary, but in the reading of her will, she has left money to the charities, and foundations that she supported, the Ring, she has left to one Rodney McKay, and absolutely nothing to John. They're literally left with nothing, the house that they live in, John's money, it's all gone, and John's wife wants to dispute the will, but John was expecting something like this, it's just what his grandmother would do, because she knew that the money was only a burden to him, that he didn't want it, but what he does want is to meet Rodney McKay. Shortly after John stopped seeing his grandmother, she met Rodney, and they became close friends, especially in the last year of her life. John wants to get to know, but what he doesn't expect, is to fall in love with him.
John Sheppard's grandmother is dying, she raised John after his parents were killed, and they've always been very close, until last year, when their relationship was strained to breaking point, and when John met and married a woman that he purposed to love. John's grandmother saw this woman for what she was; she disliked her, and rightly so, because she knows, knows that she is not who John is meant to be with, and even refused to give her, her wedding ring. John is made to choose between his grandmother, and his wife, and it's the hardest thing that he's ever had to do, but he chose his wife, who then prevented him from even visiting his grandmother, until it was too late. John's grandmother was a wealthy woman, and John is the only beneficiary, but in the reading of her will, she has left everything to John, everything accept the ring, which has been left to one Rodney McKay. Johnís wife is in heaven, and sets about spending the money with no regard for John, who only want is to meet Rodney McKay. Shortly after John stopped seeing his grandmother, she met Rodney, and they became close friends, especially in the last year of her life. John wants to get to know, but what he doesn't expect, is to fall in love with him.
While on a mission, John Sheppard gets extremely drunk, and allows himself to be fucked for the first time. He's never been with a man before, and is completely freaked out by it the next day; he's uncomfortable, embarrassed, and humiliated. John knows that he's got to hide it, from Teyla, Ronon and Rodney, and when he gets back to Atlantis. He's also worried, because it was most definitely not safe sex. When he overhears Rodney talking about something he saw last night, John mistakenly believes that Rodney saw him, and accidentally Outs himself to him. John is hypersensitive around other guys, reading too much into everything, and getting quite angry, the worst part is that he's curious, curious to explore his body that bit more, but he can't be doing this, it's not who he is. The only person he has to talk to is Rodney, and that is very awkward for them both.
When in control of Atlantis, the Replicators recreated their extension of the City into a massive complex, and teams have been selected to explore the new City. Sheppard and McKay are one of these teams, Teyla and Ronon another. It's going to take weeks to catalogue the new labs, quarters, and with more power demands, exactly how many ZPM's they're now in possession of. One thing that this is going to mean, is a much larger contingent from Earth can be stationed on Atlantis. Time spent alone together, John and Rodney realise exactly how much time they spent together before Atlantis, and when it wasn't made so easy, on earth as well. When they weren't having dinner, they were phoning each other, they do have feelings for each other, closer than either really wants to admit to, in anything other than a joking way, but is there more, and if there is, do they even want to find that out. They make the decision that while they're away from everyone else, to try being together, to test the water. The physicality is awkward, but the intimacy has always been there, what they don't know if being together is a natural progression, or if they're forcing something.
Discovering a Time Dilation Device on Atlantis, Sheppard and McKay are unaffected by its affects, as everyone else in Atlantis begins getting older, rapidly aging by decades in a matter of hours. When someone actually dies of old age, Weir evacuates the City. Escaping to the Mainland with the Daedalus' help, and once out of the Device's range, those affected begin to return to normal. Rodney and John remain to try and deactivate the Device, and although they're not aging, time is passing much faster within the City, and they're spending months together.
The Team decides to go back to the World that they found Teyla and the Athosians on, to explore the Ancient ruins that they were never able to. Inside they find a Device; that accidentally activates, causes Sheppard to disappear. It has sent John back in time, McKay is able to bring him back, but not at the same moment that he arrived. He was sent Thousands of Years into the Past, and had nowhere to go, he couldn't reverse the process, the Athosians wouldn't even arrive in his Lifetime, and the Ancients had already left Pegasus. John has been alone for a long time, and has actually gone a bit mad. His Hair has grown out, and he's acting like he's Drunk. The Team take John back to Atlantis, but nothing is working to snap John out of his state of mind, maybe nothing can. Rodney tries to get through to his Friend, but John has changed, in more ways than one.
The Wraith Mind Altering Device made Sheppard remember something else from his time in Afghanistan, that when it had looked hopeless, he and another Officer had had Sex. It's something that John has never admitted to, just chalking it down to circumstance, only Sheppard had tried to re-enact this with McKay while under the Device's influence, and are both feeling very uncomfortable with each afterwards.
An accident creates two identical John Sheppard's, with no way of distinguishing which is the original. With no way of reversing the process, it's not a bad thing, two John Sheppard's are better than one, and Atlantis benefits. The only problem is that John Sheppard had been in a relationship with Rodney McKay, and both want to continue it, but no one is willing to share, and with no way of distinguishing the original, and both of them the same, Rodney can't choose between them, and they both set about trying to win his affections over the other.