This Mortal Coil

"This Mortal Coil" is the tenth episode of the fourth season of Stargate: Atlantis.

Synopsis
When a mysterious drone crashes into Atlantis, Lt. Colonel John Sheappard and his team suspect the Asurans have found them, yet when they investigate, certain people want to stop them from finding the truth. And yet, stranger still, Dr. Elizabeth Weir returns to Atlantis out of nowhere.

Plot
In Atlantis, its Stargate has somehow been mysteriously inoperable for more than a week, around the same time since McKay was "screwing around with it". Dr. Rodney McKay and Dr. Radek Zelenka are working on restoring it. But just as they work, they hear a noise, as if something has crashed into the city. McKay puts the repair of the Gate on hold and investigates. He then discovers a mysterious probe that has somehow arrived undetected. He then notices a scorch mark, as if someone fired a Drone weapon to stop it. McKay and Zelenka attempt to determine its origins. Zelenka tells McKay it could take hours, but McKay ignores him and finds something. He sees Zelenka attempting to do something, but is stopped. McKay then sees nanite coding, when the diagnostic system crashes, losing all their data. McKay finds out that the probe belongs to the Asurans.

He runs to Lt. Colonel John Sheppard and tells him the Asurans have found them. Zelenka is with them too, but tells them that he did not see anything, and claims he had the same data readings as McKay. He insists that he saw the Base code, but as he is about to prove it, they hear an explosion. Major Evan Lorne tells them that the probe self-destructed, meaning their chance of finding any clues to the origins has gone. McKay suspects foul play.

Sheppard then goes to the gym for a sparring session with Ronon Dex. During the session, Ronon says he and Teyla Emmagan has noticed strange behaviors from other people. Sheppard just shrugs this as simple paranoia, due to inactivity from the broken Gate. However, Ronon says he is not paranoid and in the process injures Sheppard. He walks to the infirmary, where he goes to Dr. Jennifer Keller for stitches, but she says he does not need stitches, despite he is bleeding, the bleeding injury is completely gone. Sheppard wonders if he may have been infected with nanites from the probe. Keller hesitantly scans him, but sees no nanites. Sheppard then suspects that the Iratus bug retrovirus he once had in his system two years ago has reared its ugly head again. Sheppard demands a blood test when Keller starts stonewalling him.

Later, Keller and Lorne talk in a secluded place. They thought they had everything handled. Since they are far from learning the "truth", they decide to be careful. Later, Keller gives him a clean bill of health, but he refuses to ignore the fact that the cut happened from nowhere, so Keller claims that he made a mistake. When Keller leaves, Sheppard suspects something is not right, and begins to feel the same as Teyla and Ronon.

They bring McKay in. When Sheppard threatens him with a knife, he tries to run, but is stopped by Ronon and Sheppard cuts his hand with a knife. When it rapidly heals, they know that something much bigger is going on, and it's not just about Sheppard. The entire team is affected. They also believe that several key personnel on the base, including Keller and Lorne, have been acting suspicious and secretive lately. When Sheppard points out his magic healing, McKay accesses the city's medical archive, as all scans are recorded. However, he finds that the data has been erased. In order to confirm their suspicions, Teyla and Sheppard decides to sneak into the infirmary undetected, so McKay hacks into the city's Atlantis Biological Sensors to avoid Atlantis personnel. However, as he accesses the life signs, he reads only four. In order to avoid suspicion, Sheppard and Teyla continue anyway, but are noticed by Lorne, Keller and Zelenka.

Meanwhile, McKay picks up a fifth lifesign in one of the piers. McKay and Ronon investigate. Sheppard is under the medical scanner, and Teyla watches the screen. Ronon and McKay go to the area of the lifesigns, and discovers a secret door to the room. There, they see Dr. Elizabeth Weir, who was taken captive by the Asurans a few months ago. They wonder what is going on. At that moment, Keller arrives and tells them this is how they made Weir, and the rest of Sheppard's team. Meanwhile, Teyla and Sheppard confirms their fear; they are infected with nanites. There, they are confronted by Lorne. Sheppard warns Lorne, and even holds his sidearm. Lorne tells him it wouldn't do much good, and tells him to shoot anyway. The bullet causes no effect, meaning they are all Asurans.

Keller tells her group that since McKay was able to tamper with the base code, they are now able to take form of anybody they please, and took form of the Atlantis expedition. McKay knows of their first encounter of the Asurans, and that Keller hasn't been head of medical, and has never even arrived yet, but Dr. Carson Beckett was. Keller explains that she had new information from Dr. Elizabeth Weir, who was latest to be kidnapped and had her mind probed. Even the city is a copy and is on another planet.

Now in the brig, Weir proves the fact she is nanite manufactured, by cutting her hand, only to see the nanites repairing them. The replicated Atlantis team then realize that they are just test subjects for the Asurans. Teyla wonders why McKay didn't notice the fact they are on another planet, since the stars would determine their location. Unfortunately, there was solid overcast for over a week, ever since the Gate was broken.

The replicate Weir is then taken to Keller. She reveals their true purpose for the team. She informs her that the real Weir was killed several months ago because she was too dangerous. Oberoth gave her nanites to save her life. However, she used her mind and gave the other Asurans an "unhealthy influence", so Oberoth had her terminated. RepliKeller and her team are a part of Niam's faction, a group of Asurans who wish to learn ascension. Most were reprogrammed, but a small group managed to have escaped detection and stole a Zero Point Module to construct the city. They discover that since they're machines, not organic, they need the Human counterparts to study their nature and the existence of a "soul" so they can ascend. And now that Weir's team is made aware of their purpose, they plan to wipe their memories and start again. But the team plan to escape first.

RepliKeller then confronts them again, and tells them that Oberoth has sent the probe, and that now he has found them, he plans to take them back to the collective. The group refuses, so Oberoth now plans to destroy them. An Aurora-class battleship starts attacking the city. They can't raise shields, because the ZPM has used up too much power in creating the Organic Asurans. The team persuades RepliKeller to let them go, so that they can stop Oberoth once and for all. Keller lets them go. As the city shakes and collapses from the weapons fire, Keller runs to the control room and gives the team a core drive of a ships' tracking system, which should track every Aurora class ship in the Pegasus Galaxy. The team escape to a Puddle Jumper. Weir tells Keller to come with them. However, she says she may be tracked and could only be a liability. The team escape, while the city is destroyed (matching the same vision Colonel Samantha Carter received some time ago).

The Jumper cloaks and chases after the Aurora class ship and hitches a ride as it jumps into Hyperspace, thinking the ship will go to Asuras, which it does. There, McKay notices the ships they destroyed has been rebuilt, but with more being built. They land on the planet and steal a ship, which they take to an outpost on M34-227.

Meanwhile, back on the real Atlantis, Dr. Rodney McKay is working on the Stargate, when Lt. Colonel John Sheppard receives a transmission from an off-world base on M34-227. Major Jordan introduces them to a familiar face. The team are shocked and relieved to see Weir. She tells them that she is not the real Weir and that they must meet each other, as they have a way to stop the Asurans. Both teams meet, and are a little suspicious when Sheppard's team has a duplicate copy of themselves. There, the duplicate McKay presents the real team the core drive, which should track every Asuran ship in the galaxy. While the McKays work on the base, since it is a security risk to send their copies to Atlantis, the real Sheppard wants to know where the real Weir is.

There, the duplicate Weir sadly informs Sheppard that the real Weir is most likely killed. Ronon Dex and Teyla Emmagan are also mistrustful of the replicates. Meanwhile their duplicate selves are talking about their real selves. Despite Teyla telling them that since he's a duplicate, he feels himself as a lesser, but with the nanites, can go into more battles with the Wraith, where the nanites will repair him if he's injured. However, the duplicate Teyla tells him that the nanites can't heal him forever.

Sheppard and Weir talk more, when an Asuran cruiser arrives and begins attacking the camp. Weir thinks that their ship had a system, which the rest were able to track. Worse, there's another ship guarding the Gate and will take out anything they see attempting to leave through it. With the gate cut off by the Asuran ship, they need to stage a diversion if they hope to escape. The replicate Atlantis plan the diversion, to prove themselves how Human they are. They take a Jumper and uses it to distract the warships. The two chase after them, as the Stargate is dialed to Atlantis.

Meanwhile, the Jumper attempts to cloak, when the Jumper gets shot down. The Asuran patrols scout the area and found the Jumper. They enter to see the team dead, apart from Sheppard, who gets healed by nanites. He tells them "Yeah, we tricked you. But don't feel so bad. After all, we almost had ourselves convinced" before he is shot and killed. Their sacrifice has allowed the real Atlantis team to escape.

Back on Atlantis, Sheppard finally decides to remove Weir's personal effects from the city and return them to Earth, now that she is dead. Meanwhile, McKay works on the core drive for hours, trying to forget about the loss of Weir, stating it like Carson all over again. Zelenka attempts to talk to him, only to be hushed and sent away, before McKay thanks him for trying. Several hours later, Sheppard enters the lab, where McKay finally manages to get the Aurora-class warship tracker working. At first, they only see a few dots across the galaxy, until he notices more popping up. Eventually, they are shocked to discover around 30-40 Aurora class ships. During the fade-out, more beeps are heard with McKay's horror heard, saying out "oh, crap."

Notable Quotes
Sheppard: All right. Do we know what the problem is?

McKay: Yeah, the Gate's not working.

Sheppard: I think we figured that much last week when you broke it.

McKay: I did not break the Gate.

Sheppard: Oh, so it just happened to stop working around the same time you were screwing around with it.

McKay: I wasn't screwing around with it! I was running a streamlining programme designed to boost its operating efficiency.

Sheppard: Yeah, well, good job.

Sheppard: Any injuries?

Marine: No sir.

McKay: Oh thank god it hit the reading library or someone could have really got hurt.

Sheppard: Great, the last time I came face to face with my self, I ended up kicking my own ass.

Duplicate McKay: (About real McKay) Oh this is great. Finally someone who I can have 100% confidence in; I cannot tell you how much I am looking forward to working with you! And this is just the beginning but humanity is about to benefit from one of the greatest living scientific minds...x2!

McKay: Can you imagine?

Duplicate Sheppard: I'm trying not to.

(Sheppard smiles)

Sheppard double: Hold on a second. Where do you plan to do this? We're too much of a security risk to go to Atlantis.

Sheppard: He's... I've got a point.

McKay: Huh...If this works, we should be able to track every Aurora Class Replicator ship in the galaxy in real time.

(screen shows half a dozen ships)

McKay: (relieved) That's not so bad. I guess the Wraith have really taken a toll.

(more ships appear on the screen)

McKay: On.. the other hand they might have built even more.

(a lot more ships appear)

McKay: ... a lot more ...

(sounds of more ships appearing)

McKay: Oh, crap!