((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 himâ€”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 downloadedâ€”forcibly if necessaryâ€”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.