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    5x05 "Ghost in the Machine"
    Synopsis: When the city plays host to a strange computer virus, the team worries that an old enemy may have found a way to return. When they realize what it is, however, heartache and danger are quick to follow.
    Spoiler:
    ((45 second recap of "Lifeline" and "Be All My Sins Remember'd"))

    Departing an uninhabited planet, a candidate for an off-world base, Lt. Colonel John Sheppard, Dr. Rodney McKay, Ronon Dex and Teyla Emmagan approach an orbiting stargate. Muttering that this world was a waste of time, Ronon leans over and punches in the symbols for the city, hoping to get home as soon as possible. Sheppard tells him to calm down, joking that lunch will still be there when they arrive. But as the gate activates, energy levels in the puddle jumper spike. Lights flicker. Steering goes out. The drive pods won't retract. Powerless, the jumper collides with the gate and falls into a decaying orbit over the nearby planet. Another spike disables dialing capability, communications and life support. Then, mysteriously, another bolt of high voltage displacement current flashes through the jumper and restores all systems. Hastily, the team returns to Atlantis.

    After landing in the jumper bay, Sheppard and the others step out to let Radek Zelenka and a team of analysts go over the ship's systems. However, when they find no anomalies, they all come away puzzled but grateful that there are no lasting issues. John radios Woolsey and informs them that everything looks to be fine, and the city's commander replies that that can only be good. As the ex-IOA operative steps into a transporter, busy with his work, he doesn't notice the flickering lights. When the doors open, he steps out to find that a safety railing stops him—he's on a balcony overlooking one of the city's piers, far from his intended destination. Behind him, the transport doors will no longer open, his radio doesn't work, and he has no idea where he is.

    Back in his lab, McKay fields calls from all over the city about bolts of displacement current and flickering lights. All communications, both local and subspace, go offline, and electrical bolts ricochet around the city's control room. Every system is affected, and the situation only worsens when the stargate finally stops responding, too. Woolsey finally makes it back to the nerve center (having walked from the far side of the city), just as the power goes out across all piers. McKay and the science team have no explanation, though it's remarkably similar to what happened to them in the puddle jumper earlier.

    Suddenly, one of the nearby monitors flickers to life, and random letters begin appearing in combinations of Ancient and English. Confused, Teyla asks what's going on, but no one has an answer for her. McKay shouts that someone must have uploaded some sort of trans-system virus to the jumper and immediately starts taking down the network grid between all their computers. But as he stares at the screen, Chuck (the technician on-duty) realizes that he's seeing a pattern; this isn't some sort of code for an alien version of malware, it's a message slowly transcribing itself from the database's Ancient text into readable English. Seeing that he's right, McKay stops what he's doing and comes over, joining the others as they watch the note unfold itself.

    After a few more moments, it becomes clear enough to see the words "I AM FRIEND. PLEASE NO KILL." Confused, no one knows quite what to do... at least until a command prompt appears underneath the words, signaling someone to write back. Shrugging, Rodney bends down and replies, "We don't attack without need. What are you?" As if in response to show that no ill action is needed, the lights suddenly flicker back to full strength, though Zelenka notes that most other systems, including the gate, are still not responding. Over a two-way radio, a marine near the holo-room reports that the Ancient hologram generator is powering up, and suggests that someone comes down to see what's happening. Thinking that he knows what this is, Rodney leads Woolsey and the team out of the control room, explaining the the primitive speech this apparent-entity is using is no-doubt due to its incomplete control over Atlantis.

    When they arrive, they find the hologram projector coming to life... and when they see what forms, the entire group gasps aloud. For standing before them is an image of Dr. Elizabeth Weir, looking as youthful and vibrant as she did before stepping foot through the stargate on Earth what seems like a lifetime ago ("Rising, Part 1"). Upon seeing her old friends, the holo-Weir breaks into sobs of joy, falling to her knees in an emotional overload at finally returning home to the city. Not knowing what to do, the team stands in the doorway, not sure what this means for them and their mission.

    A short time later, the team is seated around the conference room table discussing their rather unique situation. Zelenka, standing at the front of the group with McKay, explains that they've firewalled the "Replicator entity" (he squirms noticeably at using that title) inside the hologram systems, but he doubts that it would actually keep "it" contained. In fact, the Czech speculates that if "it" really wanted to, "it" could simply take over the entire city again at will. Knowing this, Rodney has reluctantly organized a team at Woolsey's urging tasked with begin monitoring Atlantis's primary systems and fight any anomalies that crop up. For now, they're letting the "entity" stay in the database, but primarily only because they have no way to actually kill "it".

    Finally having enough with it, Sheppard slams his fist into the table and shouts for everyone to stop calling her "it" and the "entity." This is Elizabeth Weir, for God's sake! The woman who led them across a galaxy and sacrificed herself to save them all. Who gives a damn what the suits back on Earth tell them to call her and how to treat her; are they really going to spend all their energy trying to find a way to terminate her life? Woolsey starts to insist that they follow proper protocol, but John won't hear it. He shoves his chair back and stalks out of the chamber, despite Teyla's calls for him to stay and talk things over.

    Sighing as he watches Sheppard leave, Rodney mutters that he knew this wasn't going to go well. He excuses himself to run after the Lieutenant Colonel, leaving Radek to outline what Earth wants them to do, despite all of their reluctance to follow through. They have requested that Weir be downloaded—forcibly if necessary—and sent back home for study. If they can ascertain that she really is who she claims to be, then she will be returned to Atlantis in whatever form they can send her as. They don't want to take any chances with someone that is, essentially, a Replicator, even if it is someone who they once held in only the highest regard. Teyla admits that it does make some sense, though Ronon just shakes his head in disgust and stares off into the control room.

    Several hallways away, Sheppard is storming angrily down the corridor, shouting at people to get out of his way as he goes. McKay runs up from behind, trying and failing several times over to get him to slow down. At length, he grabs John's shoulder and pulls him around, with mixed results. On the one hand, he does turn around to face McKay, but on the other hand, he also punches him into a wall as he does so. Not satisfied, Sheppard unloads all his anger into his friend, roaring at him as to how unfair this all is and how Elizabeth deserves so much better than this kind of treatment. While he screams, Rodney slowly picks himself back up, seemingly unharmed except for a small cut along his lip, and listens silently. After another minute of this, though, John seems to lose his steam, and the man collapses onto McKay, crying over and over that it's just not fair as the two of them stand alone in the hall.

    Back in the control center, Woolsey is just returning from the conference room (Teyla and Ronon can be seen heading down an adjacent hallway in the background) when an incoming wormhole startles everyone. Once the event horizon stabilizes, Chuck announces that they're receiving the ISGC's IDC, and the gateshield is lowered to allow their visitor through. Curious, Woolsey leans over the balcony and watches as a dark-skinned man in a business suit steps into the gate room, handing a briefcase to a nearby marine and looking around expectantly. When he realizes that no one has come to greet him, the man peers up and sees the city's commander, beckoning for him to come downstairs. Warily, Richard does.

    Once he's down in the gate room itself, Woolsey recognizes the newcomer almost at once; his name is Gregory Tavares, a British diplomat and renowned interrogator. The new arrival says that he's here on behalf of the United Nations, to ensure that they extract all the information they can from the entity being referred to as "Elizabeth Weir" before they do anything with "it." He is obviously not a believer in the idea that anything should be taken at its word, and he intends to grill the hologram dry before he makes any sort of decision. Tavares asks if he can speak to the primary offworld recon team to see what they think about the situation, but Woolsey quickly stalls him with an offer to tour the city before the work begins; the last thing they need right now is Sheppard being asked why Weir should be kept alive.

    Shortly after, McKay is in his lab, going over the logs from the jumper Elizabeth jumped into and the database once she was inside it. He's hoping to find a way to defend against something like this in the future, to prevent any hostile Replicators that may have survived the destruction of Asuras from infiltrating their systems. While he types away at his computer, Sheppard enters, looking apologetic and carrying a plate with a piled-high turkey sandwich on it. He sits down next to Rodney and slides over the food, trying to impress upon his friend just how sorry he is for hitting him. He didn't mean to, but he just couldn't take it anymore and needed to get all his frustration out on something... and unfortunately, McKay was the closest "something" around. But the Canadian just laughs it off, assuring John that he went to the infirmary and had Dr. Keller check up on him, just in cast.

    While asking Sheppard what he thinks they'll do with Elizabeth on Earth, the scene fades out to one set in the holo-room, which looks significantly darker, with dimmed lights and a table set up in front of the control platform. Mr. Tavares is sitting in a chair, spreading out a few papers across the surface without so much as looking up at the image of Weir that is watching him with interest. She glances over at the marines still in the chamber and asks what his superiors have in mind for her, and when he doesn't answer, she sighs and guesses that they don't really believe that it's her, then.

    At length, Tavares shortly explains that no, the Untied Nations is not convinced that "she" really is Elizabeth Weir, who they still considered to have died on M34-112 after being shot down by the Asurans ("This Mortal Coil"). He then proceeds to ask her how, exactly, she came to find Atlantis, considering it isn't located on any world she knew about before her abduction on Asuras over a year ago. Thinking back, Weir explains that it wasn't easy; Oberoth studied her for some time, probing her mind daily and mining what information he could. After a few months of this, though, he decided that there was no point in keeping her alive any longer, and ordered his most-trusted subordinates to go to her cell and terminate her.


    (First part of "Ghost in the Machine," see next post for more.)
    Last edited by s09119; 24 August 2009, 11:26 AM.
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    Previous Episode: 11x03 "Shore Leave" | Previous Episode: 6x04 "Nightfall" | Now Airing: 3x06 "Eldest"

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      (End of "Ghost in the Machine," see previous post for start.)

      Spoiler:
      Unfortunately for Oberoth, his people were not as trustworthy as he thought. In fact, they had sympathies with the group of Asurans who had followed Niam's ascension-yearning ideals, and they faked Elizabeth's death by stabbing her through with an arm in front of their leader. Once Oberoth left, satisfied, they used a Lantean healing device to repair the wound, then ferried her offworld on an Aurora-class warship bound for the galactic rim to engage the Wraith. On the voyage into deep space, they successfully managed to deactivate the nanites inside of her, allowing her body to heal itself so she could live as a full human. Once recuperated, Elizabeth spoke to the crew, trying to make them realize that there was more to life than they had now, and that ascension really wasn't beyond their grasp. Eventually, they came to agree. They cut themselves off from the other Replicators so they could work in secret, but not before sending out a distress call in their subspace link making it look as though a Wraith fleet had destroyed their ship.

      Their next stop was a cityship that some of Niam's other followers had constructed far from Oberoth's prying eyes. But they had scarcely arrived when an Asuran probe crashed into the structure, alerting them to the fact that Oberoth was aware of its existence and preparing to eliminate it. Knowing they could still save much of Niam's legacy, not to mention the only person they had capable of teaching them about ascension, Weir's faction took on as many of their people as possible, then fled the planet just before the Replicator fleet arrived and blew up the copy of Atlantis ("This Mortal Coil").

      They spent the next few months in space, free of their brothers and sisters thanks to the alliance forged to destroy them once and for all ("Be All My Sins Remember'd"). Elizabeth taught them what she knew of shedding one's physical body, and eventually the group came to the consensus that if they dissolved their nanite bonds, they could exist as pure energy and join their creators. But many were still fearful that it would not succeed, and so Weir decided to have her consciousness transferred into a Replicator body to prove it was safe; after all, she had "died" once before, so it wasn't as though she feared the outcome. When she was able to do it, the others quickly followed suit, but before much time had passed, they found that it didn't work quite as planned. Living a torturous existence and trapped in the void of space, the group fell apart. Knowing that she was utterly alone, Weir made her way to habitable world after habitable world, praying that she would encounter an Atlantis team scouting for new allies... and eventually, she did.

      Taking notes in his book, Tavares says that he has all the information he needs for now, then gets up to leave. When he still refuses to make eye contact, Elizabeth asks why they won't believe her; the Brit's response isn't heard, as soft music suddenly swells in the background, but the tears in holo-Weir's eyes speak volumes.

      In Sheppard's quarters, John is trying to pick a classical song to listen to and calm his nerves (the music heard before), but it doesn't seem to be going very well. He just can't get his mind off of Elizabeth's return, and she's literally all he can think about. As he tosses one CD after another onto his bed, he thinks he hears her voice, and starts shouting to himself in anger, thinking he's finally going insane. But then he turns and sees the hologram of Weir standing a few feet away; she slipped past Radek's firewall and accessed the city's projection system so she could speak with him. Speaking softly, she asks why, of all her friends, he is the only one not to come and talk with her. Ronon, McKay, Teyla, Chuck, Keller, Beckett, even Woolsey, all of them came in their own time to speak with her, but not John.

      Sitting on his bed and putting his head in his hands, Sheppard says that he's not sure he can handle it. He's spent the last year trying to convince himself that she was dead, after all, and that he could never see her, hear her, touch her again. And yet here she is, seen and heard, but still little more than a dull memory, a shadow of what she once was. Upon saying that, though, his eyes suddenly light up with an idea, and he tells Elizabeth to follow him. As he rushes out of the room, she tries to shout that she can't actually move, then sighs as her hologram fizzles out.

      Weir reappears in the lab where McKay created FRAN to destroy Asuras, where John is already turning on various terminals and machines. Looking over the equipment, Elizabeth accesses the database (again piercing the firewalls) and pulls up the files on this room, realizing what Sheppard must want to do. Her suspicions are confirmed when he flip on the Replicator-making device, saying that all she has to do is override the default template and replace it with one of her own, and she could have a body again, free to walk and be real once more. And it's not like it would be that jarring, since she did it before to try and prove mechanical ascension was possible. The two of them argue the point for a few moments regardless, but Elizabeth eventually agrees to attempt it.

      The hologram disappears and the Lantean device whirs to life as metallic Replicator goo oozes out from hidden chambers, forming a silver puddle on its top. John watches hopefully, then breaths a sigh of relief when the puddle coalesces into a humanoid shape and finally a perfect copy of Elizabeth sitting on the ten-thousand year old machine and admiring her new form. She stands and goes over to Sheppard, taking his head in her hands and thanking him... and then shoving him with far-above-average strength into a bulkhead. The Atlantis military commander slams into the wall, groaning in pain, and falls to the ground, stunned and unable to move. Weir thanks him for getting her out of that annoying hologram form, then punches him in the face, knocking him out. She makes her way to the nearest armory and simply walks through the door, picking up two stunner pistols before proceeding out and into a transporter. She hits the button for the central tower, then vanishes in a flash of light.

      In Woolsey's office, Tavares is going over the information he obtained from holo-Weir (though the Atlantis team already knows this from having talked to her earlier), saying that he'll need to collaborate it somehow. Not really listening, Woolsey taps his headset and asks Sheppard if he ever filed his report on the mission to their potential new base planet earlier. When he doesn't respond, Richard grows worried, but doesn't have time to do anything; Chuck suddenly shouts that the soldiers guarding the ZPM room are under fire... from a Replicator!

      In the hallway outside the primary power room, Elizabeth is trading shots with the guards there, stunning them one by one. She looks more like a ninja than a diplomat, spinning in the air to kick one of them across the room before landing and stunning two more at the same time. She knocks the last one out with a swift kick to the ribcage, then drops her weapons, her body already repairing any minor damage inflicted by the human weapons, and enters the chamber beyond. She approaches the terminal holding the city's single module and smiles, sticking her hand into the computer system and closing her eyes.

      In the control room, a general panic has commenced. Power all across Atlantis is failing, with lights shutting off, blast doors slamming closed, and primary systems being choked out one by one. Woolsey orders anyone capable to get to the ZPM room with an ARG and to destroy the invading entity. Then, turning to Chuck, he orders the database purged of any trace of Elizabeth; they can't take any chances, not this time. He only hesitates once before nodding to confirm the order and watching as the system shutdown is initiated.

      Even with Weir's locking-down, though, there was enough time left for Teyla and Ronon, themselves on their way to dinner,to jump into a transporter and arrive on her floor. After heading to the closest armory and prying the doors apart, they grab an ARG each and make their way to Elizabeth's location, taking up firing positions of either side of the door.Then they spin into the chamber and take aim, but Teyla finds herself unable to take the shot. Knowing they have no choice, and knowing that untold havoc could be unleashed if the ZPM isn't restored, Ronon fires instead. But the waves pases right through Weir without any problem; she must have changed more than the looks of her body when she created it and installed a cipher to protect herself.

      Pulling her hand out and turning around, Weir smiles mockingly at her two old friends. She says that there's nothing they can do to stop her, and she's finally in a position to overload the power module and destroy Atlantis, getting the revenge she has always wanted on her creators. When Teyla asks what she's talking about, Elizabeth's body shimmers, turning silver, before rearranging itself into a new shape; that of the Asuran leader, Oberoth. He never died on Asuras, and instead transferred his consciousness into one of those onboard the ship that ferried Weir away from him. He did indeed take all she knew from her, and was betrayed by underlings of his who were more loyal to Niam than himself. Thanks to Elizabeth's memories, he knew exactly which Replicators were likely to be traitors, and he had no problem living amongst them for some time, traveling from world to world after Asuras was utterly devastated.

      When she discovered a possible way to ascend, she had several of her followers try it. But the plan failed, and they were trapped as electrical beings. Hoping that she could somehow help those that so-trusted her, Weir became determined to locate Atlantis so that her old friends could help her. Oberoth, knowing she trusted him, offered to begin visiting worlds that the Atlanteans would likely explore to make contact with them. Elizabeth gave him the addresses of the one's she deemed most likely, and so he went... and waited for them to come to him. She was a fool, and now he will wipe out his enemies once and for all!

      Just as Oberoth prepares to put his hand back in the power terminal, though, another disruptor wave pulses into the room... and this time, it destroys the Asuran once and for all. Teyla and Ronon turn to see McKay standing there, a slightly-different-looking ARG in his hands. Rodney explains that after the Replicators became immune to it, he and Zelenka spent months working on a new one that would be able to wipe them out again. And just a few weeks after the Battle of Asuras, they succeeded. The threat has been eliminated, for good this time.

      Some time later, McKay, Ronon, and Teyla sit in the conference room, trying to figure out how Oberoth was able to activate the Replicator machine all on his own. According to Zelenka's report on it, it's can't be remotely accessed, and it has to be initialized by a user. Stepping forward, Rodney says that it was his fault; he was doing some research on it of late and forgot to turn it off when he was done. Oberoth must have seen it active and decided to take advantage of their complacency. He played all of them, and Rodney helped him. Woolsey says that he'll need to file something about that, and that McKay could well face repercussions for nearly getting the city destroyed, but all-in-all, he didn't do it intentionally, so it seems like all will be forgiven in the long run. McKay, obviously knowing who really did do it and for what reasons, just nods, looking away and out into the gate room.

      Downstairs, Sheppard stands in the holo-room, now dark and inactive, and stares at the projector, silently vowing to find Elizabeth and bring her home.
      Last edited by s09119; 05 November 2009, 07:24 AM.
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        That's a good episode!
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        My fan-fic, swedish outpost

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          When did Sheppard turn into a 14 year old girl?

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            Originally posted by Jeffala View Post
            When did Sheppard turn into a 14 year old girl?
            It's Sheppard. He's not exactly an emotionally-stable character; we've seen him swing into rages wherever Elizabeth's life is involved.
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              Originally posted by s09119 View Post
              It's Sheppard. He's not exactly an emotionally-stable character; we've seen him swing into rages wherever Elizabeth's life is involved.
              But never emo!


              It cuts against his grain.

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                Originally posted by Crazy Tom View Post
                But never emo!


                It cuts against his grain.
                Eh, it's my opinion that in a situation like this, the former-lover of a deceased would react in this way; unable to handle the fact that the person they loved is still around, not capable of dealing with their emotions, willing to do anything they can to keep their love here before they slip away again... you can think otherwise if you'd like, but that's my interpretation.
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                Previous Episode: 11x03 "Shore Leave" | Previous Episode: 6x04 "Nightfall" | Now Airing: 3x06 "Eldest"

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                  Thats a really good episode!
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                  The replicator isnt running away, he is just, um, shifting fase

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                    Commentary re: "Ghost in the Machine"

                    Spoiler:

                    Originally posted by s09119 View Post
                    Eh, it's my opinion that in a situation like this, the former-lover of a deceased would react in this way;
                    Wow. Did I miss an episode somewhere along the way?
                    Last edited by Jeffala; 13 March 2009, 03:49 PM. Reason: To avoid spoilering--if I haven't already--the ep for Fleet Admiral - Earth

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                      Damnit i can't read this cause i haven't even seen any of Atlantis season 5 yet, it ain't aired in Australia yet and the DVD won't be here till like August or something.

                      DAMN DAMN DAMN !!!

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                        Originally posted by s09119 View Post
                        Eh, it's my opinion that in a situation like this, the former-lover of a deceased would react in this way;
                        yeah what the hell since when were they lovers???

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                          Originally posted by Fleet Admiral - Earth View Post
                          yeah what the hell since when were they lovers???
                          Aye!?

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                            Originally posted by Fleet Admiral - Earth View Post
                            yeah what the hell since when were they lovers???
                            I'm projecting my own interpretation of their relationship onto the show. They always had a romantic subplot, after all, like House and Cuddy on House. It wasn't as strongly-reinforced as Jack and Sam's feelings were, but if you ask me it was still pretty obvious (the way John acts in "The Storm," "The Eye," "Lifeline," "Adrift," etc. Heck, "The Long Goodbye" was written with them two as the alien-hostages partly to give their shippers a real kissing scene between them).
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                              good point but their relationship was more of a flirty, profesional one, and to be fair you cant really recreate another jack and sam haha. great episode
                              Captain Simms

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                                i liked it. Looking forward, as always, to your next piece.

                                Your faithful audience,
                                Check out my music on Youtube and iCompositions.com

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                                Enjoy!

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