Disclaimer: Don't own Stargate Atlantis, although I do dream of owning John, Aiden and Elizabeth, it would be so much fun.
Note: This contains SPOILERS for 'THE EYE'. I highly recommend that if you haven't seen that episode you should turn back NOW.
This is my take on what could have happened if John and Aiden didn't get to Elizabeth and Rodney in time.
Pairing: Okay this is were it gets weird. Sheppard/Weir. McKay/Weir Friendship, Sheppard/Ford Friendship and somewhat bizarrely Weir/Kolya. I promise it will make sense.
Atlantis
Elizabeth looked at Kolya
"Are you really going to sacrifice the lives of all your men on the off chance that this city won't be completely destroyed?"
Koyla thought for a moment.
"Open the Stargate, start evacuating the remaining men."
McKay, looking relived, started to activate the Stargate.
Elizabeth turned to Kolya.
"You're making the right decision"
"You're coming with us."
Elizabeth looked at him in disbelief.
"What?"
"You'll both serve the Genii as payment for what you've done"
McKay looked at him
"For what we've done?"
Two men grabbed McKay and another grabbed Elizabeth. They began to walk them down the stairs; both had guns to their backs.
"Seriously this is a bad idea! You saw what happened to my last plan; this is not what you want to do."
Koyla's men pushed McKay through the event horizon.
Elizabeth turned to Koyla
"Do you really think this is the best thing to do, Major Sheppard will come after us."
"When and if he does, he will die for what he has done to our people and you will be made to watch."
Kolya shoved Elizabeth through the event horizon just as John and Ford came into the control room. John ran to the Stargate but it shut down before he could reach it.
"Damn it."
Ford came to his side
"Sir, we need to get up to the control room now and activate the shield."
Ford looks at John and sees he is unresponsive.
"Sir, you want to help her, first we need to save the city"
Ford grabbed John's arm and dragged him up to the control room. Ford sat at McKay's computer and began to input the necessary information.
"2 and a half minutes till the storm hits Sir. Beckett and Teyla are still out there"
John activated his radio
"Teyla, Beckett fall back to the control room."
The two of them waited. The seconds passed, each knew that with each passing second the storm was getting closer to the city. After what seemed like an eternity Teyla and Sora walked in, supporting a barely conscious Beckett between them
"Activating shields now."
Ford hit a button, which began to charge up the shield generators. Ford looked at the control panel anxiously.
"Now"
The shield activated just in time to block the path of the wave, which was heading to the city.
Teyla looked around the group.
"Where are Dr Weir and Dr McKay?"
John looked at her and for the first time realised that Sora was in the room.
John, with an anger that came from nowhere, pushed Sora against a wall and held her by her neck choking the life out of her.
"Was this part of the plan? To take Elizabeth and McKay?"
Sora began to cough as she began to lose her battle to breath.
Ford grabbed the hand that held Sora's neck and pulls it back.
"Sir."
John reluctantly pulled his arm back and Sora slid down the wall coughing.
"It was never part of the plan; we came for the Wraith data device, the C-4 and the medical supplies, that's all. It was Kolya who decided to seize the city."
Teyla bent down next to Sora.
"Where would he have taken Dr Weir and Dr McKay?"
Sora looked around, reluctant to reveal anything, until she saw the look on John's face. The look told her that if she wants to live she should start co-operating.
"Properly home, although they will be waiting for you. If you try to rescue them they kill them…and you."
Genii Home World (Several hours later)
Elizabeth opened her eyes; her vision was blurry and she was unable to make out anything except for the bright light that was in the room.
"Elizabeth? Elizabeth can you hear me?"
Elizabeth winced.
"John?"
"Elizabeth it's Rodney."
Elizabeth opened her eyes fully and saw Rodney sat beside her. Elizabeth began to sit up and Rodney helped her. For the first time Elizabeth began to notice the pain in her ribs.
"Where are we? What happened?"
Rodney helped Elizabeth rest her back on the wall and she rested her head against his shoulder.
"I think were on the Genii home world, some sort of prison from what I can make out"
Elizabeth nodded
"How long have I been out?"
"Couple of hours."
Elizabeth sighed
"Any idea what they'll do to us?"
McKay sighed
"Don't think we want to know"
Elizabeth asked the question that was on both their minds.
"Do you think…they managed to raise the shield over Atlantis?"
McKay looked at her.
"Ford knew the procedure, but whether they got there in time…"
The two of them sat in silence.
TBC…
I already know how every bit of this story is going to be written so the whole thing will be posted within a week, 2 weeks at most.
