Disclaimer: I don't own Stargate: Atlantis. If I did, it wouldn't be cancelled at the end of this season.

Summary: What if Elizabeth and the other Replicators had decided to stay in Atlantis to create their human bodies instead of leaving at the end of "Ghost in the Machine?" How would the season then turn out? With Michael gathering his forces, Todd coming up with a surprising solution to the problem of the remaining Wraith (minus his hive, of course), and a surprising lab in the city concerning biological weapons against the Wraith, Sheppard and company will be have to keep ahead of everything or be left behind in the new order of the Pegasus Galaxy. AU.

It was later, back in Woolsey's office. John and Elizabeth had hurried back after the destruction of Koracen to find all of the other Replicators sitting sedately in the work room they had set up. Most were shocked, and some were miserable about the accident; mostly because Koracen had set this all up and broke the Lantean's trust, some because of the results of the plot. Koracen had been well liked by some of the surviving Replicators.

"So what now, Elizabeth? Do you want to stay and keep working, or do you want to leave?" That was Woolsey, who had been ready to ship all the rest of the machines home after he learned of the double-cross, but once John and Elizabeth had told him of Koracen's fate, he calmed down. Particularly when he saw that several of the others had gone back to working on the machines to build human bodies. Going straight back to work with no further interruptions impressed him.

"I think that we should leave. If Koracen could betray us, so could any of the others. IT's too risky."

Woolsey made a face. "To be perfectly honest with you, I don't see much problem with the others. They just went straight back to work, and have almost completed the mind transfer device, as Doctor McKay has informed me."

Elizabeth smiled briefly. "And how long did he take to inform you?"

Woolsey rolled his eyes. "About fifteen minutes. Between complimenting the efficiency of Replicator workers and whining about how it was too bad humans weren't like that, he barely had time to say what he originally tried to tell me."

"I guess some things never change. Did I ever tell you about the time he sent me thirty-something emails about why we should have kept another Z.P.M on Atlantis instead of sending it back to Earth?"

"I'll bet that was fun."

"Not really. But as you were saying; yes, we have made some progress, but we still are a major security breach." Here, Elizabeth cast a nervous glance at John. Woolsey turned to him also. Rodney, Ronon, and Teyla walked up then and started staring at John as well. Now John became nervous. "What?"

Woolsey adopted his "answer-me-now" face. "Colonel Sheppard, you are the ranking military officer on this base. You have a say in this, too. Right now, if you say it's too dangerous, then they would probably leave, with or without asking."

Elizabeth broke in with "John, I know you don't trust me, but please believe me when I say that we are not your enemies. Just give us another chance."

Rodney probably then made up John's headache from being thrown into a wall by Koracen come back when he popped up with "Come on, John, if it works, then they'll be the same as us. Would you trust them more if they were human?"

John was starting to feel overwhelmed when Teyla said "I agree with Rodney. Also, I believe that this is truly Elizabeth, and that she is our ally."

The Colonel had pretty much made up his mind, but he needed one more opinion. "Ronon, how 'bout you? What do you think?

Ronon glared at the Replicators that were standing below in the Gate Room. They're Replicators, Sheppard. I don't trust 'em." Here, his face became a little softer, if possible. "But since Doctor Weir let me stay here when I found you guys, I'll give her another shot at it. I owe her that."

Elizabeth was surprised that Ronon would allow her this. She turned back to John to await his decision. Deep down, she hoped that John would let them stay, but the practical part of her nanites knew that that might be too much to hope for. She heard John take a deep breath and, despite what his team had said, braced herself for the worst.

"Okay. I'll let you guys stay."

Elizabeth started and looked up at him in hope. John raised a finger. "However, there will be some restrictions, like before." Elizabeth nodded eagerly. "There will be a number of forcefields around your lab, there will be guards with ARGs outside the lab at all times, and once the human bodies are completed, your machine bodies will be destroyed, so there's no way to go back. Agreed?

Elizabeth and Woolsey both nodded in agreement. "Agreed. We will not get in your way at all. However, once we are finished, what will you do with us then?"

Woolsey spoke up at this point. "At that point, I see no problem integrating you with the rest of the base- under guard for the first week or so, of course. If you want to leave or stay after that is your choice." The unspoken question hung in the air: And what of you, Elizabeth? Will you stay with us or go with the others to ascend? However, the awkward moment was passed by as Elizabeth rose, saying: "I will discuss this with the others; it is their choice as well.

"Very well." Woolsey looked pleased.

In the end, the Replicators decided to stay. A few had voted against staying, obviously feeling uncomfortable around so many humans, as well as being under guard, but they were swayed by the others. They then headed back to their lab to try to complete the equipment needed.

John and the team stood with Woolsey in his office, watching the last of the Replicators get what they needed. Woolsey then turned to John and said quietly, "I hope you're right about this."

"Me too. At least Koracen's gone."

--Commercial break--

It was a week later, and everything was looking up. Most of the machines needed to build the new bodies were either completed or almost finished. Earlier in the week, John had spoken to the prophet- er, McKay, and asked for a timeframe. Rodney's response was positive. "Normally, with humans building this type of technology, it would take a hell of a lot longer time than it would for our guests. They don't need food, sleep, bathroom breaks, and they know exactly what they are doing. The perfect workers. If only we could create more that could work for us…"

"Hey, careful, Rodney. Remember the Terminator movies."

"Ha-ha. Very funny. Now if you'll excuse me, I have a Z.P.M. to build."

"Really? Given up on recharging them like last time? Maybe you're growing some sense, after all. Just don't bring another parallel universe copy of yourself here again."

"Sheppard?"

"Yes?"

"Leave."

That was a while ago, and John was now roaming the city for something to fiddle around with. Normally, that was McKay's job, but they hadn't gone exploring for a while, and John was bored. He walked the city until he found that he was in a recently unflooded section of the city. They had never been this way, preferring to stay in safe territory.

John kept walking until he found a single door at the end of a hall. He went through, and had the shock of his life:

Wraith. Wraith bodies in stasis boxes around the wall. There were several computer panels on the walls, and some on pedestals in the center of the room. After a closer look, John realized the all of the Wraith were dead; all with various needle puncture marks and some with mutilated features. John grabbed his radio.

"This is Colonel Sheppard. Get Doctors McKay and Keller down to my location right now. I've found something they should see.

--Commercial break --

"It's a lab. A lab concerning biological weapons against the Wraith. Some were injections, some were bombs. Any way they did it, however, it didn't work." That was McKay after a very thorough investigation.

"Why didn't it work?" Woolsey asked. He had been shocked when he entered the lab and saw all of the Wraith bodies.

Keller stepped in at that point. "It was actually based on a Lantean version of Carson Beckett's retrovirus. The drug or gas would tear away the iratus bug genes in the Wraith, destroy them, and then actually deteriorate the human cells until they died. That was the original idea, and it worked well in injections, but the gas form didn't exactly work as well."

"And why not? From what I can tell, there seems to be no problem."

Jennifer turned a little green when she voiced her response: "The problem was that any humans or Ancients caught in the blast would suffer the same fate as the Wraith. When you think about it, it's almost the same as the Wraith feeding process, without the draining of the life force: age the cells, and the victim dies. Apparently some Ancient had a twisted sense of humor; kill the Wraith with their own feeding technique."

Woolsey also turned a little green. "That is… disturbing. Is there any way you could make the bomb so that it only affected Wraith?"

"Well, one way would be to beam it onto a Wraith ship, and then hightail our asses out of there." John helpfully put in. Ronon, behind him, grinned appreciatively.

Rodney clicked his fingers at John. "Uh, Colonel, remember? E.M. field around all Wraith ships? No beaming in or out?"

John shrugged. "Maybe we can get the Replicators to help us."

McKay was about to reply when a lieutenant came through the doorway, saluted, and then addressed Mr. Woolsey and John: "Sir? I got a message from the Replicators? They've finished all their equipment and want you to know they're almost done. Apparently, they'd like you to be there when the bodies are built."

John nodded. "Thanks, Lieutenant." The man nodded and walked away. He turned to Woolsey and the team. "Well, guys, let's go watch some machines build humans. He walked out the door, hearing McKay's parting shot: "Machines building humans? Sounds like a Terminator movie in reverse! Movie freak."

John chuckled.

A.N. Phew! That took a while to write. I've had this story idea bouncing around my head for a couple weeks, and have decided to finally put it down on paper- figuratively, of course. Anyway, I've got a question for you to put in your review: Should Elizabeth get her new body to look like her old body, or should she stick with FRAN's image? I'm leaning toward her keeping FRAN's image, myself. And of course, please review or I'll send Michael after you and turn you into a hive ship. That's a promise.  Bye!