Outcomes and Consequences

A/N: This is my take on how "Allies" could conclude. It doesn't match any of the synopses out there at this time.

Disclaimer: Stargate: Atlantis, its characters and terms, are the intellectual property of others. This is an amateur effort with no infringement intended.

Missing

"Shit, that was close!"

Lt. Colonel John Sheppard looked out from his position behind a bulkhead to see wraith darts returning to the landing bay. He had only just been able to hide the F/302 in the back of the hive ship's bay before the first of the darts started returning. Fortunately for him, they were on auto pilot and were taken to the launching tubes automatically.

His next thoughts were unprintable as he realized why the darts had returned: the ship had just gone into hyperspace. He was once again on a hive ship, but this time he didn't know where it was headed.

"Well, more time to find Rodney and Ronon," he thought. With the lack of activity in the landing bay, Sheppard eased back over to the F/302 and took stock of his supplies. Besides the gear in his vest, he had the survival kits under the two ejection seats in the fighter. The equipment was similar to that in an F/16: water, radio, signal flare, knife, compass, etc. He was glad that they added food to the gear since he didn't think he could "live off the land" in a spaceship. He used the camouflage net to cover the F/302, softening its lines to blend in with the organic look of the hive ship. He repacked his vest with Power bars, the knife, the 9 mil and all available ammo, and sat with his eyes closed, visualizing the layout of the hive ship and where his team was likely to be. He'd give anything for a life signs detector and a P90. But he knew this rescue would have to be done the old fashioned way: with a grid search and with stealth. Checking his watch so he could keep track of the elapsed time, he set off to search for his lost teammates.

Daedalus

The mood on the Daedalus was grim.

"Sir, course plotted for Atlantis."

"Thank you, lieutenant, stand by." Turning slightly, Colonel Caldwell glanced at the Asgaard member of his crew. "Hermiod, do one more sensor sweep. Is there any indication of debris from an F/302?"

"No, Colonel, the only debris is wraith craft."

"So he might still be out there."

"I'm picking up neither life signs nor vessels at this time."

"Humor me, and do one last sweep." Caldwell settled back into his seat. "I'm the one who has to tell Dr. Weir that I lost both her chief scientist and her chief military officer."

"Yes, Colonel Caldwell," said Hermiod, as he leaned over his controls.

Atlantis

"You're sure they got all the gate addresses, including Earth?" Dr. Elizabeth Weir stared intently at Radek Zelenka, willing him to say something else. They had moved the discussion to her office.

"Yes, Dr. Weir. We must assume that Earth's location has been compromised."

"Can their ships make the trip?"

"Yes, they are comparable to the Daedalus if a little slower."

Dr. Weir closed her eyes in resignation as she stepped out of her office to address the technicians in the control room. "Raise the Daedalus as soon as she's in range."

"Yes ma'am," said the technician.

Hive ship

John Sheppard moved cautiously down the dark halls of the wraith ship. Without the life signs detector, he could not be sure where the wraith were, nor could he find Rodney and Ronon easily. Therefore, he had to check every cell and cocoon. He had decided to move forward from the landing bay, thinking that Rodney would have been near the bridge at the time the ships jumped into hyperspace. He still didn't know why the automatic beam out device had not worked, but most of this mission had gone to hell, so what was one more snafu.

Hearing footsteps approaching, Sheppard ducked behind a pillar, holding his breath and blending into the darkness. He had been fortunate so far, having avoided the wraith. With only the 9 mil handgun he knew he couldn't overcome them easily, and he didn't want to alert them to his presence until he was ready to leave, preferably with his team members intact. As the pair of wraith passed, he eased back into the corridor, reminding himself to keep an eye out for water and food while he searched the ship.

Atlantis/Daedalus

"Daedalus, this is Atlantis. What's your status?"

"Dr. Weir, this is Colonel Caldwell. We are about 8 hours out. The alliance was a sham, and we were attacked when we came out of hyperspace."

"That is not a surprise. We found a virus in the information downloaded from the wraith. The virus destroyed all the information they had sent to us."

"One moment doctor." Caldwell looked to his lieutenant who began to input queries as she checked the onboard database. She looked up at him and shook her head.

"Our data is also gone," said Caldwell. "So we lost that tactical advantage…"

"It's worse, Colonel. They also took all the gate addresses in the ancient database."

"But they already know where most of those worlds are…"

"No, Colonel, I mean they now know how to reach Earth."

There was a pause as Caldwell considered possible responses.

"Do your scientists have any idea how long it will take them to get there?"

Weir looked to Zelenka who nodded and picked up the conversation.

"Colonel Caldwell, this is Dr. Zelenka. The wraith hive ships do not have ZPMs so their propulsion is comparable to that of the Daedalus under normal drive conditions. They are, however, a little less powerful, so the 18 day trip of the Daedalus will take a hive ship around 22 days.

"OK, that means we have a little leeway. Dr. Weir, have you informed the SGC?"

"Not yet, Colonel, we were going to give you two hours to check in before sending a data burst."

"We will continue on our present course. Please have all data ready for transmission. We will add our tactical information on the two ships that took off. See you in 8 hours, Dr. Weir. Daedalus out."

"Atlantis out."

Weir turned to Zelenka. "Get everything together for a transmission. I'll go complete a report on what happened. Also, check with Dr. Beckett to see if he has any additional information on the wraith physiology."

Zelenka nodded, stepped to the doorway, then looked back. "I wonder why the colonel didn't ask Dr. McKay about the speed of the hive ships?" He shrugged and hurried off to compile the needed information

Elizabeth Weir stood frozen for a moment. The blood drained from her face as she realized the implications of that remark. Then she shook herself and moved over to her desk. She opened her laptop and began writing her reports.

Hive

Lieutenant Colonel John Sheppard had been on the hive ship for 8 hours and had completed the search of one half of one deck. He had decided to work his way forward and back to the landing bay in a zigzag pattern. That way he could use the landing bay as a base. There were very few wraith in the landing bay while the ship was in hyperspace, so it was the best place to rest. After the first swing, he realized he had been awake over 24 hours and needed some down time. Eating half of a power bar, with a little water, he set his watch for six hours, put it under his ear, and curled up under the edge of the camouflage tarp covering the F/302. In spite of the stress, he immediately went to sleep.

Atlantis

"Atlantis, this is Daedalus requesting permission to dock."

"Permission granted, Daedalus," acknowledged the technician in the control room. "Dr. Weir would like to see Colonel Caldwell, Colonel Sheppard, and Dr. McKay as soon as possible in the conference room."

"Acknowledged, Atlantis. Daedalus out."

Caldwell shook his head, squared his shoulders, and left for the briefing.

In the briefing room, Elizabeth Weir was staring into space, trying not to panic as she waited for the crew from the Daedalus to arrive. Just as she was about to get up and pace, Colonel Stephen Caldwell entered the room and came to stand in front of her. He was alone.

Elizabeth stood up carefully. "Hello, Colonel. Where are the others? I don't want to start…"

"Elizabeth," said Colonel Caldwell.

She blanched. Caldwell rarely called her Elizabeth, and usually didn't interrupt her.

"They aren't coming. McKay and Dex did not get off the hive ship before it jumped to hyperspace. Colonel Sheppard was in an F/302 engaged with the hive before it left. He disappeared. We found no trace of him after the battle."

Elizabeth sat down suddenly, staring into space.

"…all of them?"

"Yes. I'm sorry. I am listing them as missing, presumed dead."

Elizabeth continued to stare at the wall, all color gone from her face. After giving her a few minutes, Colonel Caldwell continued.

"Dr. Weir, is the data ready for the transmission to Earth?"

"What? Oh, yes, Colonel. My report has been attached to Dr. Zelenka's, and we have included all scans of the ship. Is your report ready?"

"Yes, I'll have my lieutenant transmit it now." Suiting action to words, he contacted the Daedalus for the information.

"Dr. Weir, we have received the data from Daedalus," said the control room technician.

"Acknowledged." She tapped her earpiece. "Dr. Zelenka, this is Weir."

"Go ahead Dr. Weir," said Zelenka.

"The data from the Daedalus is being transferred to you at this time. Please put it with our data and prepare the message for Earth."

"I've received the data and am now running the compression algorithms. I will be up shortly. Zelenka out."

"He's putting it together now, Colonel," said Weir turning to face the Daedalus commander. She was still pale, and her hands trembled slightly, so she clasped them together on her desk.

Caldwell nodded in acknowledgement. "I leave the transmission in your capable hands. Now, I am going to make best speed back to Earth since we probably have an attack on our hands."

"Good luck, Colonel," said Weir, as she turned to her laptop, not really reading the screen.

Caldwell hesitated, then reached over and grasped her shoulder. He was gone before she even recognized the gesture.

Dr. Zelenka, standing in the control center, watched Colonel Caldwell leave Dr. Weir's office and leave for the docking pier. He waited a few minutes, then approached her office and knocked. She startled slightly and looked up from her laptop, bidding him enter. To be fair, however, she had not read a word on the screen for the last fifteen minutes.

"Dr. Weir, the data has been sent to Earth. We were able to save some small parts of the wraith schematics before the worm totally destroyed them, so we sent those along as well. With the scans from the Daedalus it might be enough information for Earth to mount a defense." Dr. Zelenka paused, not sure if she heard him.

"Thank you, Dr. Zelenka. I know Earth will appreciate your efforts." She continued to stare at her laptop.

He hesitated before leaving, and she noticed. Glancing up, she said, "Was there something else?"

Hesitating again, Zelenka asked "Uh, did Colonel Caldwell mention taking Rodney with him?"

Startled again, Elizabeth realized neither Radek, nor anyone else on Atlantis for that matter, knew that Sheppard, McKay, and Dex were missing. Yes, presumed dead, but she didn't have to tell them that yet.

"Dr. Zelenka, Colonel Caldwell said that the Daedalus was attacked on emerging from hyperspace and Dr. McKay's automatic beam-out device did not work. He considers Rodney and Ronon missing."

Zelenka sat down hard in the chair in front of her desk.

"What about Colonel Sheppard? I did not see him either."

Elizabeth swallowed. "He is missing as well." She paused. "Radek, I need to inform Teyla before she hears from someone else. Please don't mention this situation yet. I will send out an official notification soon."

Zelenka nodded. "Yes, Dr. Weir." He stood up. "I'll just go back to the lab now and continue working on the wraith data."

"Thank you Doctor." Tapping her earpiece, Elizabeth Weir spoke again. "Teyla, Major Lorne, and Dr. Beckett, will you please report to the briefing room?"

She heard their acknowledgements and closed her laptop. Then she leaned her elbows on her desk and put her head in her hands. How was she going to explain to them something she couldn't accept herself?

Hive ship

The sound of his watch alarm in his ear jerked John Sheppard awake. He was disoriented at first, then he realized where he was and the adrenaline surge finished waking him up. He took a few minutes to consider his search activity. He had started forward because Rodney would have been near the bridge. Also, from his memory of the hive ship schematics, as well as previous experience, he knew the aft area was mostly engines and storage. He remembered the ship had around 20 decks, but at least five were wraith "quarters" or storage, or whatever they called their living/hibernation space. Even searching half of the ship, 15 decks would take awhile. Grabbing his gear, he set off to make another swing forward.

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... to be continued