Ghost In the Machine

Summary | Production | Transcript | Fan Reviews

The city of Atlantis becomes host to the minds of disembodied Replicators, led by someone very close to the team.

FAN RATING - 8.54 
NIELSEN - 1.2 
DVD DISC: Season 5, Disc 2
WRITTEN BY: Carl Binder
DIRECTED BY: Ken Girotti
GUEST STARS: David Nykl (Radek Zelenka), Michelle Morgan (Elizabeth Weir), Robert Moloney (Koracen), Leanne Adachi (Lia), Chuck Campbell (Chuck), Richard Busch (Marine)
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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. 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.

As Radek Zelenka and McKay find no problems with the Jumper, Sheppard briefs Atlantis commander Richard Woolsey on the ordeal. As Woolsey goes his own way, he steps into a transporter. Busy with his work, he doesn't notice the flickering lights. When the doors open, he steps out. A safety railing stops him – he's on a balcony overlooking one of the city's piers, far from his intended destination. The transport doors will no longer open, his comm doesn't work, and he doesn't know where he is.

Back in his lab, McKay fields calls from all over the city about bolts of displacement current and flickering lights. City-wide communications and the Stargate go down, and electrical bolts ricochet around the city's control room. Every system is affected. Woolsey finally makes it back to the control room (having walked from the far side of the city), just as the power goes out city-wide. McKay and the science team have no explanation, though it's remarkably similar to what happened to them in the Puddle Jumper.

A lone laptop reboots, and the team watches as garbled strings of letters resolve into the words "HELP" and "ELIZABETH WEIR." Stunned, McKay ascertains that this entity is the same computer malfunction from the Jumper, and that it has overwhelmed even Atlantis's network. Creating a large program to gather the entity in one place, McKay also gives it a voice. It is not just a computer malfunction, but an entity that has inhabited the city – and she claims to be Elizabeth Weir, the former expedition commander who was lost to the Replicators over a year ago ("Lifeline"), and presumed dead ("This Mortal Coil").

Weir recounts her experiences since being captured. Although her nanites replaced her remaining organic cells and remade her into a full Replicator, her consciousness remained intact. Niam's group (rebels seeking to learn the secrets of ascension) understood this when they created human duplicates of her and of Sheppard's team ("This Mortal Coil"). They were saved when the Replicator homeworld imploded ("Be All My Sins Remember'd"). Finally free of their leader Oberoth's oversight, they pursued their goal of ascension.

Their technological nature left them unable to participate in the biological process of ascension – until one of them, Koracen, found a technological solution. By dissolving the nanite bonds, their energy was released into subspace. As pure energy, they should move to the next plane of existence.

It didn't work. As disembodied entities living a tortuous existence, they searched the galaxy for a way to regain physical form. They found other technologically advanced societies that are hiding from the Wraith, but no solutions. They even checked Wraith technology. In the end, Weir knew that Atlantis was their only hope.

Ronon and Woolsey are suspicious. Sheppard wants to place her consciousness in a virtual reality, as they have done with Replicators before ("Outcast"). But before anyone can act, Weir discovers the Ancient device used to create the first humanoid Replicators (which Rodney made use of last year), and creates a body for herself. She downloads her consciousness into the last template stored – Fran, the "Friendly Replicator Android" created by McKay ("Be All My Sins Remember'd").

Even more concerned now, Woolsey wants Weir transferred to a virtual reality. McKay wants to keep her functional, since he created the problem by reactivating Weir's nanite cells and feels he needs to rectify that decision ("Adrift").

Meanwhile, Teyla visits with Weir, sharing news of her son's birth. Tasked with escorting Weir back to the lab, Sheppard is warned that the other disembodied Replicators are now coming to Atlantis. Without enough time to prepare, the city's computer network is overwhelmed and commandeered by Koracen and the others. He demands the use of the Ancient technology to manufacture new bodies. When Woolsey refuses, Koracen starts to submerge the city into the ocean, threatening to kill them all. Woolsey stands firm, declaring that human and Replicator will die together if Koracen persists.

Weir devises a plan whereby basic model Replicator bodies will be built, without the ability to replicate or heal themselves. Once downloaded, they would create the machinery to make mortal, human bodies into which they would transfer their consciousnesses – believing that human element is needed to finally ascend. With strict protocols in place, Woolsey agrees. As the Replicators work on new bodies and download themselves, Ronon, still deeply suspicious, keeps watch. His vigilance pays off when Koracen disrupts power to the city and escapes the containment area.

As Ronon pursues him, McKay tries to regain control. Koracen, unwilling to shift to a human body that will die, wants to find another way – a technological way to ascend. He knocks out Ronon.

Sheppard discovers that not only did Koracen escape, but so did Weir. Now believing he can't trust her at all, he orders the rest of the Replicators destroyed. Lia, acting as spokesman, points out they are still in the containment area, that they are honoring the agreement. Sheppard relents and sets off to find Koracen and Weir, leaving Major Lorne and his men to watch the Replicators closely.

When Sheppard locates them, Koracen tells him that most of this was Weir's intent from the start. Weir truly thought they would be no danger to Atlantis, and so she called them there. Sheppard tells her may think she is Elizabeth Weir, but she isn't. Putting the city in danger from one of its worst enemies proves it. As if to demonstrate she is the real Elizabeth, she pins Koracen to a wall and forces her fingers into his forehead, dissolving his nanite bonds and killing him.

Now convinced that she and her people are a danger, Weir leads her companion Replicators through the Stargate, supposedly to a safe place where they can work on human bodies. But the gate has been secretly reprogrammed – with Weir's knowledge and content – to send them to a space gate. As each Replicator follows her through the event horizon, they drift, deactivated by the cold of space. Something of the real Elizabeth had remained in this Replicator incarnation after all.

- S. Fetter


  • Actor Robert Moloney, who plays Koracen in this episode, made his first Stargate appearance as Borren, one of the Aschen, in the SG-1 episode "2001."
  • Leanne Adachi plays the Replicator Lia in this episode. She would go on to the recurring role of Corporal Barnes on Stargate Universe, appearing in ten episodes.
  • "Ghost In the Machine" was written by staff writer/producer Carl Binder, who joined the staff a couple of months late this year following the Writer's Guide of America strike. Binder is the only member of the writer's staff who is a U.S. citizen and member of the WGA.
  • The episode was originally written for Torri Higginson's Elizabeth Weir. Higginson was a main cast member for the show's first three seasons, and then reduced to a recurring role – appearing in four episodes of Season Four. The producers sent her the script for "Ghost In the Machine" hoping she would return to continue the storyline introduced in the final moments of "Be All My Sins Remember'd," but the actress turned down the offer.

    As a result, the script was rewritten so that the cliffhanger could be resolved and the story continued without her – bringing in actress Michelle Morgan as the reincarnation of Elizabeth in a Replicator body. See below for comments from both Higginson and executive producer Joseph Mallozzi.
  • "Hey, look who's back! Yep ... Carl Binder turned up for work today! And he brought us a present: his first draft of 'Ghost in the Machine.'" (Executive producer Joseph Mallozzi, in a post at his blog)
  • "Last year, after we shot that final surprise scene in 'Be All My Sins Remember'd,' I stopped by Torri's trailer to congratulate her on a job well done and, also, to assure her that the door was left wide open for Weir's possible return (in some form, be it Repli-Weir or other) the following season. Torri was excited by the prospect and, in particular, had great things to say about her new leather outfit (props to Val).

    "As Season Four wrapped, Carl and Paul [Mullie] got to spinning and came up with a terrific storyline that picked up where that last scene of 'Be All My Sins ...' left off. We had a story in place for one episode, the starting point of a potentially bigger arc. The script was written and we eventually contacted Torri who, after much consideration, turned down the offer to reprise the role of Elizabeth Weir for the episode. We are, of course, disappointed, but nevertheless respect Torri's decision and wish her all the best in her future endeavors." (Executive producer Joseph Mallozzi, in a post at his blog)
  • "I've just finished a nice six-day run out at The Bridge Studios. ... Two episodes in those six days: 'Ghost In the Machine' and 'The Shrine.' Some nice McKay/Zelenka scenes in there. Two great eppies, too." ("Zelenka" actor David Nykl, in a post at his blog)
  • "That storyline we are going to follow through on – but we will not be seeing Torri [Higginson]. When last she was in town for 'Be All My Sins Remember'd,' it was a very short scene, and she was at the time very excited that we had left the door open for her character. So based on her response we wrote the script. But when we went out to her she ultimately elected to pass. Which is fine – we don't want to force anyone to do the show! However, given the script, given the plot, it was possible to do the story without her. So Carl went back and did a rewrite and the story will go ahead.

    "It's unfortunate – the fans would have liked to have seen her for continuity's sake, but at the end of the day it's Torri's decision and we respect that." (Executive producer Joseph Mallozzi, in an interview with
  • "I'm not coming back. They did come to me and ask me to come back this year, but it was very unclear as to what it was going to be, what they're going to ask you to do, and it was unclear as to if it was going to be a tidying up of her or if it was going to continue to be a vague 'Is she here, is she not there?' And so that, mixed with other contractual things, I chose not to do it.

    "And it was sort of tough, because I felt a sense of responsibility – and mostly, to be honest, towards the fans, I wanted to give them a sense of closure. And I felt that I was sort of being betraying by saying no to do it, but I didn't feel it was going to be a closure. I wasn't convinced it was going to be, it was going to tidy it up. So I felt, well then, if we're just going to continue this sort of vague dragging it on every year ... And I wanted a clarity, and I thought that at the end of the day, however much the fans might be disappointed and not have her do it for another episode, I think they would appreciate my reasons why. I hope so." (Torri Higginson, in an interview with Big Finish Productions)
  • "The last time Torri was on the show late in Season Four, she seemed genuinely excited at the prospect of the new storyline (and the fact that we hadn't closed the door on Weir). Based on that reaction, we went ahead and wrote 'Ghost In the Machine.' In the interview cited [by a fan], Torri states she didn't want to commit to a guest appearance because 'it was very unclear as to what it was going to be, what they're going to ask you to do, and it was unclear as to if it was going to be a tidying up of her or if it was gonna to continue to be a vague 'is she here, is she not there.'

    "Surprising, given that she did receive a copy of the script. She followed up with a request for some sort of closure for the Weir character. After some discussion, we let her know we would accommodate that request. But, in the end, she decided to pass anyway." (Executive producer Joseph Mallozzi, in a post at his blog)
  • "I understand the fans' desire to support Torri, but I don't find it fair or helpful to speculate on the reasons for her declining the offer. As I wrote in yesterday's entry, we fully respect and support Torri's decision and wish her all the best. For the record, however, it wasn't a specific script issue. The content of the script (which has yet to be delivered) was never even discussed." (Executive producer Joseph Mallozzi, in a post at his blog)
  • Is Weir conscious, floating through space, or did her systems shut down? "Her system – and the systems of her fellow Replicators – have shut down. However, if anyone is foolish enough to mount a recovery and then attempt to awake them, they'd be asking for trouble." (Executive producer Joseph Mallozzi, in a post at his blog)
  • Before Atlantis was cancelled, Carl Binder intended to write an episode that brought back Elizabeth Weir once again in the show's sixth season, according to Mallozzi.
  • "The reason we brought back the Weir character was in order to tell a story – potentially a series of stories – that fans of the character would enjoy. While I think closure it certainly nice, I'd argue that fans would have preferred to leave the door open and seen the character make multiple reappearances rather than ending Weir's story. For instance, the scenario ... 'Team Sheppard successfully rescues Weir and brings her home to Atlantis to recover and rejoin the team?' is not a conclusive end to the storyline but a continuation in a different creative direction.

    "In my mind, the original Weir was not destroyed (as the human form Replicators would have us believe). Her body was kept 'on ice' somewhere to serve as a prototype for future study. At the time I wrote 'This Mortal Coil,' I imagined a future storyline that would have involved the team learning of Weir's fate and launching a rescue op. They would have retrieved her and, in the end, Elizabeth would have headed back to Earth for some R&R, leaving the door open for future guest appearances." (Executive producer Joseph Mallozzi, in a post at his blog)