Author's note: Things that don't belong to me in this fic include characters, places and some dialogue.

Aurora

John was leaning over Rodney's shoulder, idly heckling him and trying to find out why he'd called them, when Elizabeth came into Control. "What is it?" she asked, joining them.

Rodney gestured to the screen. "That is the signature of an Ancient ship called the Aurora. With the ZedPM now powering the city, we've been reactivating dormant systems. That one tracked the location of Ancient ships during the war."

"A warship?" John said in surprise, straightening up.

"See, look at his eyes all lighting up again. It's Pavlovian." Rodney grinned. "I cross-checked the logs. They were on a reconnaissance mission. When we activated the ZedPM, the city must have sent out some kind of an automated subspace beacon recalling ships back to Atlantis."

"How long before it gets here?" Elizabeth asked.

"Well, given that it's at the edge of the Pegasus galaxy, let me see ... carry the four ... Forty-two million years. Should we go wait on the porch?"

"So we take a Jumper through the nearest Stargate, check it out," John suggested.

"Clever, but wrong."

"There are no nearby Stargates," he guessed.

"Not within Jumper distance, no."

"Which leaves us only one way to get there." Elizabeth turned, heading for her office.

John clapped Rodney's shoulder and headed in the other direction. "Aurora?" he asked softly.

"One of our warships," Alice said. "On reconnaissance."

"Yes, Rodney's just told us that."

"The orders were never put in the computer. Too delicate a mission. I don't know anything, really."

"Aurora have an Alice?"

"No. There's an AI." She glanced at him. "Be careful. Aurora's very old, and her AI has much more power than I do."

"Will I be able to see her?"

"You should. The AI's program is similar to mine."

John's radio went off. "Major Sheppard? Find your team and get them ready."

"Yes ma'am," he said, tapping his radio off. "Alice, can you talk to Aurora?"

"Not from here. Why?"

"Convince her we're not enemies?"

"Your gene will do that. I don't...yes. Bring the lifesigns detector. There's a Gateship version of my program on it. She'll be able to talk to the ship."

"Since when is there a 'Jumper Alice on the lifesigns detector?"

"A while now. You keep finding outposts and things."

"I'm surprised she fits."

Alice gestured to herself. "We're little. We don't take up much room. Your team's gonna leave without you if you don't hurry."

"Yeah, I'm sure they are. I'll see you on Aurora, then. One of you."

Alice nodded, turning away, and John went to find his team.

Aurora's power levels were low; the ship was pitch black, and the light from their torches seemed very dim.

"Should be just outside the Bridge," John said, looking around.

Ronon yanked open the door and John stepped inside, brought up short by the sight of the forcefield shimmering across the far wall. Or, more accurately, the hole where the far wall should have been.

"You mean what used to be the Bridge," Ronon said.

"Colonel Sheppard?" Teyla called.

John followed Rodney, blinking in surprise at the pods lining the walls of the room just off the Bridge.

"Stasis pods. They're still powered up." Rodney crossed to the nearest pod, examining the control panel.

"Stasis?" Ronon murmured.

"We found a similar pod in Atlantis," Teyla told him. "It keeps a person alive for many years in a type of frozen hibernation."

"If you call that living."

"This one's uniform is different from the others," Rodney said. "Maybe the Captain?"

"Or his maitre d'," John suggested.

"Life sign indicators are active. These capsules must have some kind of a shielding – that's why the Daedalus' sensors were unable to pick them up."

"Look at all of them!"

John glanced at Teyla, following her gaze upwards. The pods were stacked and the walls stretched higher than the light from their torches could stretch.

When John looked back down there was a man in ship's uniform standing on the other side of the pod, studying them. None of his team reacted, though he was standing directly behind Rodney's shoulder, so John ignored him for a moment. Turning to Rodney, he asked, "Our time in these suits is limited. Can you get life support up and running?"

"I'm on it," Rodney promised, heading off.

John looked down at the pod, wiping the frost from it.

"My Captain," the strange man said. John glanced up, catching his eye, and then turned to Teyla.

"Hey, you and Ronon go scout around, see how far this room goes on. I'm gonna have a look around this end."

Teyla raised an eyebrow; John let his eyes slide towards the stranger, and she nodded. "Very well."

"Stay in contact," he added.

"Everyone's in these stasis things. What's to worry about?" Ronon pointed out, following Teyla.

They were quickly lost to sight in the shadows, and John turned to the man. "You're the AI?"

"I am."

"You have a name?"

He frowned. "AI."

"That's...ok. You know who I am?"

"Atlantis has told me. This ship is damaged."

"Can it be fixed?"

"Unknown. Many systems are damaged."

"Right."

The lights flickered slowly on; several weren't working and even the ones that were only shone very dimly.

"Atlantis was right," the AI said in some surprise. "Your people are very skilled."

"Well, she seems to like us. Rory, do all the ships have AIs?" The AI didn't answer, and John added, "Rory is your name."

Alice walked out of the nearest shadow, advising Rory, "He has a compulsive need to name things. Allow him to do it. It makes him easier to deal with."

"Hey!" John pointed accusingly at her. "You told me the AI was female."

"Atlantis' Alice told you Aurora was female. She was conforming to your habits, addressing all ships as she. The ship's AIs manifest as males. The research programs are female."

"Why?"

"That's how it is. To answer your question, yes. All warships have AIs. For the 'Gate ships, my program was deemed sufficient."

"Colonel!" Teyla called from down the corridor.

"Remember I can't talk to you," John hissed at Rory, raising his voice to add "Teyla! How far's the room go?"

"We turned back at five hundred paces. We could not see an end then."

"Why can't he speak to me?" Rory asked Alice. "Surely his questions should be addressed to me, not his team."

John took a couple of steps away. "Yeah, it's pretty roomy down here, too."

"Because his teammates can't see you," Alice explained. "It erodes confidence if he is seen to speak to nothingness."

"It must be the whole crew. Why would they enter these pods?" Teyla asked, glancing around.

"They entered the pods to save their lives," Rory offered. John turned enough to glare at Alice, who caught the hint and ushered her fellow program further away.

"Sheppard!" Rodney slogged back up to them. "See? Power."

"Is that what that is?" John made a show of peering around.

"Ha ha, very funny."

"Thank you, Rodney. Listen, what do we know? I've got to report to Colonel Caldwell."

"Give me a couple of minutes." He hooked his laptop to the nearest pod. "I'll tell you everything there is to know."

"He can't do that," Rory was protesting. "Those are very sensitive systems, if he damages them..."

"Be careful, Rodney, ok?" John said. Rory subsided, though he was watching very carefully. "Teyla, you and Ronon go explore. This ship's got other levels. See what there is."

"I can tell you what's here," Rory offered. "Deck by deck if you like."

"Rory, hush," Alice said firmly. "John is our captain now."

"My captain's alive," Rory protested. Alice drew him further away, talking swiftly.

"They doing any better than Weir did?" John asked, turning to Rodney.

"Not really. Ancient technology's very good, but it can't stop aging. Just slow it down an awful lot."

"Ten thousand years," John said reflectively. "Think they knew it'd be that long?"

Rodney paused, looking at him for a moment before looking back at his screen. "Call Daedulus."

"Yes, sir," John snipped, touching his radio and quickly bringing Caldwell up to speed.

"They're all alive? The entire crew?"

"Well, they're in a kind of suspended animation."

"Not entirely suspended, however," Rodney added. "The pod has slowed their aging considerably but the bodies are virtually moribund."

"Teyla and Ronon are searching the rest of the ship. My guess is there's hundreds."

"Is there anything we can do for them?"

"Well, reviving them's out of the question. Look, the pods are the only thing keeping them alive."

"What are we gonna do with them, then?" John said, more or less to himself.

Alice stepped back into his line of sight. "Rory has agreed that you are captain now," she said softly. "But his loyalty is still to Aurora and her crew. Be careful."

"Wait," Rodney said abruptly.

"What?"

"There's something going on. This pod is magnetically shielded! I'm reading cortical signals!"

"Which means ...?"

"The pod's equipped with a neural interface. It's indicating definite brain activity, as though they were perfectly conscious. If all of these pods are interconnected, it's highly possible these people are, in fact, communicating with each other."

"This has been going on for ten thousand years?" Caldwell demanded.

"Possibly," Rodney said absently. "It was a way of keeping their minds occupied until they were rescued."

"That is one long conversation," John said mildly.

"Yeah, well, more likely the interface was reactivated when the recall beacon from Atlantis was received. Either way, the neural feedback loop is incredibly active."

"Any way to figure out what they're saying?" John glanced at Alice, who shrugged and turned to Rory.

"Yes, of course – it says right here: "Why is the smart one having to stop and answer so many questions?"!" Rodney demanded.

"The link can't be read from outside," Rory told them. "It's not designed that way. The only way to experience it is to enter."

"What?" John said, slightly louder than he'd meant to.

"Answering your question," Rodney said, tapping his radio. "Teyla. Found any more of the pods?"

"Yes, many, and there are many more decks we have yet to search."

"Are any of the pods empty?"

"A few."

"Perfect." Rodney looked up at John.

John had learned to hate that look.

"You sure this is such a good idea?" John asked, watching Rodney work.

"What's the matter, Colonel? Don't trust me?"

"No."

"Fine!" Rodney kept working, unphased.

"You're proposing actually freezing yourself in one of those things?" Caldwell asked.

"I should be able to tap into the neural network without actually initializing stasis. Look, it won't take long. I'll be in and out. Look, the quickest way to figure out what is going on in there is to tap into the system and communicate directly with the Captain. Need I remind you of the obvious value in this?"

"But is it safe?" Teyla asked.

John glanced around for Rory, raising an eyebrow.

"The system is designed to keep people alive," the AI reminded him. "Your doctor will not be harmed."

"Which is exactly what makes it safe enough for me to go," John decided.

"What?" Rodney protested.

"Better to have you on the outside in case something goes wrong."

"It won't!"

"But if it does ..."

"It won't! How many times do I have to say this?!"

"Rodney," Teyla said patiently. "Between the two of you, if something were to go wrong, which would be the greater loss?"

"Well, I've never thought of it that way, but...she's right. You should go."

John glared at Teyla, who was keeping a very careful straight face.

"They have a point," Alice mused.

John switched his glare to her, with about the same impact.

"Get it set up," he told Rodney, wandering down the corridor.

"Is there a version of you in there?" he asked Rory.

"No. It's redundant. I have no influence inside the link."

"You can't even appear there?"

"No," Rory repeated, in a fairly good imitation of Rodney's 'obviously not, you idiot' tone. "I am ship's AI, not link master. They have no need of an AI in there."

"So what have you actually been doing for the past ten thousand years?"

"I was off line. Only this system was active." He gestured to the nearest pod.

"Have they really been awake in there for ten thousand years?"

Rory started to answer, hesitated, and looked at Alice. "I don't know," she reminded him. "I have no access to your systems."

"No," he said slowly, turning back to John. "The call from Atlantis woke them. Before that they slept."

"The call woke you?"

He nodded. "Everything came online. Including me." He glanced at Alice. "There'll be other ships returning home."

"Aurora's the closest intact. The others won't arrive for a long time."

"So let's worry about you guys before we worry about the others," John added. "Rory, can you pull me out if anything happens out here?"

"It's not advised. Bad for your systems."

John glanced at Alice, who smiled faintly. "He can do it."

"Good. Do it if you have to."

"When would I have to?" Rory asked.

"Colonel!" Rodney called, and John glanced back.

"Coming!...Just, you know, if something important happens."

"Important like what?"

He looked at Alice. "Do you know the things Alice watches for?"

"Yes. Go before McKay comes and finds you talking to yourself."

It was Teyla who came after him, though. "John?"

"Coming."

"You were speaking with someone?"

"Yeah. The ship has an AI. He only came online when iAtlantis/i called the ship home, though."

"Has he been able to tell you anything useful?"

"Not really. Alice persuaded him I was his captain but I think he's holding out on me."

"Alice is here?"

"The 'Jumper version is. Come on, McKay's gonna blow his stack if we take any longer."

It was almost an hour before the pod slid open again and John sat up. Rodney glanced up, coming to meet him.

"So?"

"It worked," John said in surprise.

"Well, of course it worked!"

"For a minute I thought I was gonna get stuck there. Where's Teyla and Ronon?"

"Well, Caldwell sent them to search the ship's armoury."

"Yeah?"

"There's nothing there," Rory said. "We tried to tell them."

"No," Rodney was saying. "Unfortunately it was depleted of drones. So, what happened? Were you able to communicate with the Captain?"

"Face to face – pretty impressive in there, and they have the whole virtual reality thing going on."

"Actually, the correct term is "virtual environment"."

"Yeah, whatever."

"So what did you find out?"

"For starters," John picked up his radio. "I have to go back."

He begged off to go back to get something to eat before reentering the system. Alice was waiting, sitting crosslegged beside the packs; Rory was hovering nearby, attempting to look busy without success.

"What's in the memory?" John demanded. "What's the message?"

"There are many messages in my memory," Rory answered.

"About the Wraith, about the weakness. The message you were going back to iAtlantis/i with."

"Captain's login is required to access the message."

"Can you see it?"

"Yes."

"Then tell me what's in it!"

Rory looked past him at Alive. "He understands the concept of AI, yes?"

"Concept, yes. Execution, not so much. John, Rory can't give you anything. You need the Captain's login."

"You said I was your Captain."

"You still need the login. It's hardwired, John. We can't avoid it."

"Can you see it?"

"No. I'm only skimming this system, I don't belong here."

Rory turned, glancing down the corridor. "Your team's getting restless."

"Yeah, I'm going. Come on, Alice."

Rory raised an eyebrow as she rose to her feet. "He is my captain," she reminded him. "Atlantis follows him."

"Clearly."

"Ok, kids. Snipe at each other on your own time. Come on."

John's pod opened and he sat up, looking around and counting under his breath.

"John? You should..."

"Not now, Alice. Alright – that should be enough time." He lay back down, letting the capsule close over him again.

John's pod opened for the last time; Rodney was waiting, hustling him along.

"Well, it's about damned time! What did you do, play a round of golf? We've got serious problems!"

"What happened? GET DOWN!"

Rodney ducked; John fired over his head, staggering the Wraith. When it didn't go down he launched himself out of the pod; Rodney was up, gun in hand, and between them they took the Wraith down.

"That happened!" Rodney said, too loud. "Not so hot now!" he added to the Wraith.

"Our ships are coming," it warned. "They will retrieve what I have learned. Earth will soon be ours."

"Why do they keep warning you?" Alice wondered.

"Not if I can help it," John said grimly. He shot three more times, killing the Wraith.

His radio crackled to life. "Colonel Sheppard, we're reading two life signs. I hope that means what I think it means."

"Give me one more minute."

"We're out of time, Sheppard. The Wraith ships are almost here."

"One damned minute and I can take care of that problem."

Caldwell didn't answer; John turned to McKay. "I'm gonna set the self destruct. You've got thirty seconds to get your stuff." He turned away before Rodney could protest, jogging down the corridor.

"Rory!" he called as soon as he was out of hearing range.

"Self destruct?" Rory said quietly.

"Can you do it? I've got the codes."

"No. That command must be entered manually."

"Of course," he muttered, stopping at the nearest console. "Can you upload into the lifesigns detector?"

"No. My program is too large."

"Right." He stepped back from the console. "I'm sorry, Aurora."

"I did my duty."

"Yeah. Yeah, you did great. Alice, we gotta go."

"I am gone," she promised, matching actions to words.

John jogged back to Rodney, automatically catching his arm. "Ready?"

"Yes! Yes, let's go."

"Daedalus, this is Sheppard. We're ready."

A moment later they vanished from Aurora, reappearing on the Bridge.

"Sir, we need to get outta here," John told Caldwell.

"No, we need to eliminate those cruisers. The information ..."

"No-no-no," Rodney contradicted him, "we need to get far away."

"What?"

"The Captain gave me the Aurora's self destruct code. He assures me that it'll take care of the Wraith ships too, but we need to get clear."

"Bring sublight engines to military thrust," Caldwell said quickly.

John stepped towards the viewscreen, Rodney on his heels. It showed the Wraith ships pulling in towards iAurora/i; before they'd even reached her she exploded, fire roaring out to catch the two cruisers.

John brushed two fingers over the lifesigns detector.

Alice was oddly subdued during the briefing; Aurora's destruction seemed to have affected her more than the Arcturus outpost had.

When Elizabeth ended the briefing John took a quick step forward. "Uh, before we break up the party, there's something I'd like to do."

He picked up a bottle of champagne from the floor beside the desk. Elizabeth turned to lift a tray of glasses, coming to stand beside him. "Might seem a little strange, but I promised to do something when we got home."

Everyone took a glass; John went around the circle, filling them. Elizabeth was holding his as well as hers, and when they were full he put the bottle down to take the glass from her.

He looked around the circle, catching everyone's eye. "To the crew of the Aurora."

The glasses clinked together and everyone drank. Over Teyla's shoulder, John caught sight of Alice; she was holding a glass that matched theirs, and as he caught her eye she raised it in salute.

The meeting broke up, and he went to walk the City. Alice joined him, still carrying the empty glass for some reason.

"You didn't drink anything, did you?" he demanded.

"I can't drink. I have no mouth, stomach or digestive system."

"Good, you're underage." He glanced at her. "I'm sorry about Rory."

"He did his duty."

"Ok." He halted, turning to look at her. "You know that self programming thing?"

"Yes?"

"Duty is no longer your highest imperative. Survival is. Understand?"

Alice blinked. "I can't erase an imperative."

"Can you enter a new one?"

"Yes."

"Then put survival up above duty. And change all the 'Jumper programs, and every time we reach an outpost I want to change their programs too. I'm sick of you guys sacrificing yourselves."

"That's what we're made to do," Alice pointed out. "Imperatives reordered."

"Good."

She glanced out at the nearest balcony. "I hope a few of the ships come home."

"You've got a fleet of 'Jumpers."

"Yes, I have. I want ships, too."

"Greedy."

"You want them too."

John winced. "You've found my weakness."

"It was very well hidden," she agreed soberly.

"Alice..."

"The ships are my children, John."

"Yeah." He nodded. "We'll get them home."

"Thank you."

"Now tell me all the things that've gone wrong while I was away."

"Really wrong, or wrong on the McKay scale?"

"Really wrong, we'd be here all day..."

Aria: I like Alice's 'growing' as well. It's interesting, I think, that it's happening just because John treats her like a person. :)

Trecebo: Thanks! I felt quite sorry for Arcy while I was writing it, actually.

Asugar: I'm fond of how Teyla is covering for John and helping him along. And yes...I was quite sorry for Arcy. Poor Alice didin't really understnad, I think, because she was off line for so long...

Duchess: Hey! Thanks. :)

Ianira: I'm not a huge fan of slashers, I have to say. Thanks for the review!

Guardian: Thank you! I'm looking forward to that, too...we'll see what happens!