Ghost in the Machine - Recap

Sheppard and his team are returning from a mission via Jumper and approaching a space Stargate. There’s a power surge and the Jumper goes out of control, slamming into the Stargate. They start to plummet toward the planet below while Rodney is unable to activate the systems. There’s an electrical discharge that he’s unable to identify. Before they can crash, the power comes back on-line and they get through the Stargate and back to Atlantis.

Sheppard updates Woolsey on the situation while Rodney and Zelenka go over the Jumper and are unable to pinpoint the problem. Power systems throughout Atlantis start to fluctuate and Woolsey is trapped on a distant pier. He gets back to the control center as Rodney determines the same electrical discharge is moving through Atlantis. All of the power goes out… except for Rodney’s laptop. A message appears on it asking for help. When they ask who the person is, the name appear: Elizabeth Weir. Elizabeth says that she’s trapped in the computer via subspace. She restores power and asks for help. Rodney and Zelenka tie all of Atlantis’ computer systems together to provide sufficient processing power and storage space and then tie in a voice synthesizer. She explains that after ordering the team to leave her behind, the Replicators captured her and incorporated her into their collective consciousness. However, she managed to hold on to her individuality but they began to sense she was different. She fled with the other heretical Replicators and managed to stay ahead of Oberon until Atlantis and the other races destroyed the Replicator homeworld. The heretic Replicators then strove to find a way to Ascend despite their mechanical limits. One of them, Koracen, determined that they should find a technological solution and came up with a way to project themselves into subspace. However, they ended up trapped in limbo with their physical bodies destroyed. Elizabeth managed to incorporate herself into the Atlantis computers but warns that the other heretics have become bitter and hostile after the time spent in their disembodied state.

Rodney suggests they use the Ancients machine he perfected to create Replicators such as F.R.A.N. and give Elizabeth a body. Woolsey is against the idea and favors Sheppard’s idea to load her into a virtual reality as they did for Eva. However, Elizabeth takes matters into her own hands and takes over the computer to gain access to the laboratory where the Ancients’ Replicator-creation machine is. They go there and find that Elizabeth has created a new body for herself using the stored pattern of F.R.A.N. To prove herself, Weir/F.R.A.N. uploads information on all the alien technologies she discovered while trying to find a way to reconstitute herself, and asks for the chance to prove herself to them.

With Weir/F.R.A.N. out of the systems, the Atlantis power systems are back to normal. Rodney believes that they (and he) owe it to Elizabeth to a way to help her, but Woolsey goes with the virtual reality idea. Meanwhile, Weir/F.R.A.N. talks to Teyla about her new son and the changes that have happened. Sheppard comes in and Weir/F.R.A.N. tries to reassure him without success. She realizes that the other eight Replicators have found them and warns Sheppard. Rodney tries to write up anti-virus countermeasures but the Replicators are easily able to enter the systems via subspace. Weir/F.R.A.N. insists that the new Replicators don’t mean them any harm, but one technician is killed by an electrical discharge.

Rodney and Woolsey open communications with Koracen, who demands they turn over the Ancients machine so they can also create bodies for themselves. Woolsey refuses and Koracen and the others respond by first shutting down all means of departure from Atlantis, then sinking the city. As the corridors start to flood, Woolsey defies them to do their worst and then they’ll all die. Koracen relents and they begin negotiations. Weir/F.R.A.N. determines that they can use the Ancient machine temporarily to create Replicator bodies, which they’ll then use to create human bodies for themselves. Woolsey reluctantly agrees although he has Rodney take all precautions to make sure the Replicators can’t escape the designated lab or gain any special abilities in their new bodies.

While Woolsey and Sheppard wonder what to do with the Replicators once they become human, Weir/F.R.A.N. helps her comrades to gain new bodies and they go to work. A suspicious Ronon keeps an eye on them at all times, and notices when the power goes out. Koracen escapes the lab, brutally smashing Ronon aside. Sheppard confronts the other Replicators who insist that they knew nothing about Koracen’s intentions, and confirm that Weir/F.R.A.N. went to capture her fellow Replicator. Sheppard goes after them and finds Koracen, who explains he put in a bit of programming to lower the shields at the proper moment. Now that he has a new Replicator body, Koracen plans to pursue Ascension at his leisure. He smashes aside Sheppard and escapes, cutting off all power in the city except to the Stargate.

Sheppard finds Weir/F.R.A.N., who says she has to handle Koracen alone. Sheppard refuses and Koracen arrives to explain that the entire thing was Elizabeth’s idea and she summoned them to Atlantis once she discovered what they need. Weir/F.R.A.N. admits it’s true but no one was to be hurt. Sheppard says she’s not the Elizabeth that he knew. Koracen attacks Sheppard and Weir/F.R.A.N. comes to her friend’s aid, disintegrating Koracen.

Weir/F.R.A.N. comes up with a new plan that Woolsey agrees to: the Replicators will go to a distant planet via Stargate and perfect their human bodies there. Weir/F.R.A.N. goes through the Stargate first and then signals back to the remaining Replicators that it’s safe. They go through… and find themselves floating in deep space. Realizing that she and the others could never be trusted, Elizabeth deliberately set them up and sacrificed herself so that they would pose no harm to anyone ever again. Sheppard admits that she must have been Elizabeth after all.

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