The alternate, tragic, slash ending. I just had to write it. Original rating still applies. Warning for character death.
McKay didn't stop talking when Caldwell entered Weir's office.
"I swear, Elizabeth, it was only a few times, we aren't – there's nothing going on now. It was just – just stress relief, you know? Just two guys helping each other out, letting off a little steam. I didn't tell you because there's nothing to tell. There's no reason for any investigation, no reason for John – for Sheppard to be punished." McKay was wringing his hands, his voice shaking. He turned frantically to Caldwell.
"You said you'd help. You'll put in a good word for him, explain that he was just doing it to help me? Sheppard isn't gay, you can't – you can't accuse him of that. It isn't fair. You can't let them ruin his career because of me."
Elizabeth turned a stern gaze on Caldwell. "You didn't tell me there was an investigation going on. I don't appreciate being left in the dark and made to look like a fool. You should have come to me first, Colonel."
He thought furiously, stalling for time by clearing his throat. "I did, Doctor Weir, and you shut me down. You insisted that Doctor McKay and Colonel Sheppard were not involved in any kind of inappropriate relationship. But the facts proved otherwise, and I felt my only recourse was to confront Doctor McKay. I'm trying to help them, Elizabeth, not condemn them."
"This is all my fault," McKay moaned, sitting down abruptly. "I didn't know you hadn't told Elizabeth about this, you should have said. I just wanted to let her know that I was taking full responsibility for everything. Here," he snatched a CD off Weir's desk and handed it to Caldwell, "my confession. And my personal guarantee that it will never happen again."
"Will that be enough, Colonel?" Elizabeth asked. "I'd hate to see this become an issue, and believe me, it could be very bad for everyone. There are too many civilians and military personnel on Atlantis from countries that don't have such restrictive and discriminatory policies about homosexuality for any kind of disciplinary action concerning it not to cause a great deal of unrest and upset."
"I certainly hope so, but I can't guarantee anything. If Sheppard is relieved of command, I'll do my best to make sure the reason why doesn't become popularly known. We do try to be discreet about these things." Inside, Caldwell was exultant, but he carefully preserved the mask of friendly concern.
Shortly afterward, as he stowed his gear in his quarters on the Daedalus, he carefully locked McKay's precious confession in his desk. Command of Atlantis was as good as his, or at least, not in Sheppard's reckless hands any longer. Success had wiped away all his doubts like they had never existed. McKay would be upset for while, certainly, but Caldwell had no doubt that he could handle the scientist's uncertain temperament. Hadn't he skillfully manipulated the man into giving away himself and his lover, while having no proof at all?
He slipped the key to the desk into the hole, and felt a sudden, intense pain travel from his fingers, up his arm, and into his chest, leaving a trail of freezing cold behind it. His legs folded beneath him and every muscle seemed to spasm at once, leaving him sprawled on the floor. Unable to move, even to blink or breathe, he couldn't feel his fingers or his toes, then his hands and feet, numbness creeping up farther and farther until he felt he was just a consciousness gazing out of blurred eyes. He didn't feel the lack of air in his lungs or the slowing beat of his heart.
A shape moved into the fixed field of his vision, and he heard a voice whispering in his ear.
"It's a neat little device, don't you think? Works instantly. Unfortunately, the records left by the Ancients indicate that it has no effect on the Wraith, even though it works perfectly on humans. Absolutely undetectable, too. Completely paralyzes you while leaving you awake and aware, then triggers a neat little brain aneurysm. Makes you wonder just what the Ancients really intended it for. It serves my purposes, though, because it gets you out of the way without any suspicion of murder."
He couldn't make out the face in front of him as his eyes dried out and his vision faded into blank whiteness, but the high, sharp voice was unmistakable.
"I can't let you do it. I can't let you take him away from me, do you understand? My parents are dead, my sister is gone…I need him, Colonel, and he needs me. I can't believe you actually thought I'd fall for it. There is no investigation, is there? You started this all on your own. You have no evidence except my confession. Elizabeth will keep her mouth shut, the last thing she wants is someone else in charge of the military on Atlantis.
"Did you forget that I'm a genius? Go up against me, Colonel, and you'll lose. In fact, you've already lost. In a moment, you'll be dead, I'll remove the device I planted in your desk and my confession, and no one will have any idea that your death wasn't completely natural. Such a tragedy, but those aneurysms are almost impossible to detect, aren't they? I've already programmed the security cameras so they won't record me moving around on the Daedalus, and if I meet up with anyone, well…I'm supposed to be here, aren't I? One last check on the drive systems before takeoff.
"John Sheppard is mine, Colonel. Nothing is going to change that, and no one is ever going to take him away from me." His hearing was fading now, too, along with the last remnants of conscious thought, but the low chuckle was still audible. "You lose, Caldwell. Everyone who goes up against me loses, sooner or later. And you lost the moment you delivered that letter."
A/N: Okay, this really is the end. Hope you had as much fun as I did, and thanks so much for all the lovely reviews and feedback. Words can't express how much I appreciate you all.