The Seed

"The Seed" is the second episode of the fifth season of Stargate Atlantis.

Synopsis
When a mysterious alien organism takes Dr. Jennifer Keller as its host, the newly revived Dr. Carson Beckett and the crew desperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis. In the meantime, Richard Woolsey officially joins the team, having been chosen as Colonel Samantha Carter's replacement to lead the Atlantis expedition.

Previously on Stargate Atlantis
The team finds Dr. Carson Beckett after he was thought to have been killed a year previously, only to find out that he is a clone. His cells were degenerating, and with no other solutions, they were forced to put him in a stasis pod. Soon, the team found Michael's database, which could allow the Atlantis expedition to finally defeat him. However, his base self destructed, leaving several team members trapped. Colonel Samantha Carter helps rescue them, and, exhausted, returned to Earth for an review from the International Oversight Advisory on her first year in command. Despite a good evaluation, she learned that Richard Woolsey would replace her to lead the expedition.

Plot
Teyla Emmagan is walking with her new born son, Torren John Emmagan, who is asleep, but in order to do so, Teyla would have to walk while holding him. She passes a tired Dr. Jennifer Keller in the infirmary, where she is looking through Michael's database for the cure on Dr. Carson Beckett's condition, and thinks she may have found something. Teyla came to thank her for reverting the Hybrids back to Humans, and she had a chance to see Kanaan earlier today. Keller tells Teyla that Dr. Rodney McKay often talks with Beckett in the stasis pod, telling him of the latest news. Keller once caught McKay, who was then pretending to look over the systems. Torren starts to wake up, and Teyla gets moving again.

Meanwhile, in the control room, McKay, Lt. Colonel John Sheppard and a team await for Richard Woolsey's arrival. He is then beamed down from the Daedalus. However, instead of a speech, he asks for his belongings to be sent to his quarters, and orders McKay to send him his latest reports. Sheppard sarcastically comments on his "nice speech" to the team, before going his own way. At night, Keller has fallen asleep, and wakes up. As she gets up, she notices that her right hand is covered a mysterious gelatinous goo. In horror, she quickly gets up and washes it away. She decides to turn in and sleep in her quarters.

The next morning, the team, apart from Woolsey enters the conference room, where they quickly notice that the table is replaced by a twelve foot long mahogany one. The team thinks why Colonel Samantha Carter was relieved of her command, since she has done exceptional work with the destruction of the Asurans, and the weakening of the Wraith. Sheppard thinks that is the problem. Since much of the threat has disappeared, the International Oversight Advisory felt to be put in control, since the threat level of the galaxy has gone down. Essentially, Carter has become a victim of her own success. Woolsey enters the room, and tells everyone to be seated. The group discuss several topics, including the events over M2S-445. However, all but Woolsey know that Michael Kenmore may have escaped through the Puddle Jumper that went missing, and one of his ex-mercenaries reported to have seen him after his cruiser was destroyed. Woolsey deems the source too unreliable, and moves on to the next topic; the former Hybrids. Despite Teyla telling him that they are actually victims, Woolsey says they were also enemy combatants, and are to be held on the mainland until he deems them trustworthy to roam around.

The final topic is the status of the clone of Beckett in the stasis pod. A distracted Keller tells him that she thinks she has found a serum that can stop his cellular degradation. Unfortunately, it has only been tested on lone cells, not a live person. The only way to test it is to put Carson out of stasis and inject him with the serum. Despite the risk that Carson may die the second he exits stasis, they go ahead with the procedure. They enter the stasis room, and deactivates the stasis field, where Beckett falls into the gurney. Keller quickly injects him with the serum, and sends him to the infirmary. They wait, when Beckett eventually wakes up. He sees his team again. Keller reports some good news; there are no signs of cellular degeneration, he's in the clear. By the end of the day, Keller goes to her quarters to get some sleep.

The next morning, Beckett takes the opportunity to look at the city skyline. McKay confronts him and tells him that they plan to send him back to Earth to recover from his condition. Beckett seems fine with it, believing that he is still some time away from being in top shape again. They are then interrupted by Teyla from the headset. She wants their help. She tells the two that she went to Keller for a breakfast date, but couldn't get an answer. She assumed she was still asleep, and now she is late for her shift. McKay manages to open the door, where they see Keller asleep, with no sign of her waking up. Teyla notices something, and pulls out the bed covers and is shocked at what they see, tendrils covering her stomach.

Sheppard and Woolsey are called into the situation. Beckett says that he saw this once before, when he was Michael's prisoner. They move both her and the bed, since the tendrils are attached to the bed as well. They discover that the tendrils are actually growing from inside her. Woolsey lets Beckett stay, despite being scheduled for Earth, and that he is not an active expedition member, but has more experience in Michael's experiments. Sheppard tells Woolsey that this "isn't by the book". Woolsey tells him that they must not get used to it. Beckett operates on Keller, and cuts off a small tendril. Unfortunately, her vitals shut down. The surgical team try their best to revive Keller, which they did. Beckett tells the team that he will not attempt that again, since it may kill her. Beckett takes a blood sample and discovers that she has been infected by a Wraith pathogen. Later, Keller eventually wakes up.

McKay enters the isolation room in a Hazmat suit, and discovers that the mass has multiplied in size. Keller is visible afraid, and can't go to sleep, through fear of not waking up again. She experiences numbness all over her body, and hears mysterious voices, which are most likely in her head. Beckett tests the blood samples on everyone that has been in M2S-445, and discovers they are all infected with the pathogen. The infected members are restricted to quarters, and Carter has been quarantined in Stargate Command. Woolsey still has not decided what to do with Keller.

Beckett finds out what the pathogen does, and presents his findings to Woolsey. The pathogen is comprised of a organo-metallic polymer, which overtime, will go hard enough to resist hyperspace radiation, and the material is similar to that of Wraith spaceships, meaning that a Hive Ship is most likely coming out of Keller. Due to this new threat, Woolsey orders the entire tower Keller is in evacuated. Another problem is that the tendrils are growing very rapidly. Teyla talks to McKay, who figures out the the tendrils are growing to get access to more power, where it well go too quick to stop it. He believes the tendrils are heading for a power source, a power conduit leading directly to the Zero Point Module. Teyla tells this to Woolsey, who assembles a team to examine the advancing tendrils. Beckett also starts work on how to stop the pathogen.

Dr. Radek Zelenka, Teyla and a team are investigating the area, and Zelenka splits off from the team and watches the tendrils attached to a wall, that has attached itself onto the power conduit. As Teyla is coming, the tendrils sense Zelenka's presence and attacks him, knocking him to the floor. Just as he is overwhelmed, Teyla fires her P90 onto the tendrils, which are retreating. She takes Radek to safety. With this information, Woolsey decides to have Keller terminated. Fortunately, Beckett invents the serum, a phage, which should kill the pathogen. The downside is, there is no way to test it. Sheppard volunteers to be tested first. He is restrained on a bed if anything happens. He is injected with the phage. At first, he doesn't feel anything, but soon starts to violently convulse. Eventually, it stops, and Sheppard returns to normal, with the pathogen completely gone.

Woolsey decides to break the rules again, and decides to send someone to the isolation room to inject Keller. Unfortunately, there are several tendrils in the way. Ronon Dex volunteers, since he is infected, the pathogen in Keller would detect no threat from him. Ronon takes the phage with him, and starts his move. He goes into a transporter. The second he enters another section, the ZPM is pulled, blacking out the city. Ronon walks past the tendrils with no sign of being harmed. He then encounters a shell in front of him. With no other way, Ronon decides to shoot his way through, against Beckett's wishes. He shoots through the shell, where the tendrils detect that he is a threat. He uses his sword, but is stopped and pinned down to a wall, where they start to strangle him.

With the plan going awry, Sheppard makes contact with Keller. However, he hears a more deeper-alien version of Keller's voice. She tells him that she is not Keller any more, and when she is completed, she will have her own designation. Sheppard gets the team to buy time, so he could fly a Jumper. He flies it and sees that the entire tower Keller is in is completely covered in the mass. In a daring course, Sheppard flies the jumper straight into the tower and crashes. He arrives just outside the isolation room. He arms himself and makes his move. He quickly moves into the room, and injects Keller with the phage. Keller quickly wakes up in pain, and the tendrils eventually loses its hold of Ronon, who falls. However, as the mass dies, a tendril stabs Sheppard in the stomach. An injured Sheppard is about to kill Keller, until the tendrils stopped moving.

Sheppard is in the infirmary, recovering from his injury. Woolsey tells him that Ronon has a bruised larynx, meaning he will lose the ability to speak for several days. Sheppard comments "wonder if anyone'll notice". They then see Keller, who is now up and about, back to normal. Beckett arrives and says he is ready to go back to Earth and thanks Woolsey. He then talks to John and expresses his disappointment in himself for breaking at least half a dozen security protocols during his first week, but if he didn't break them, Keller would be dead, and the city will be in serious trouble. His superiors at the IOA decide to let the matter drop. Woolsey firmly believes that the rules are "there for a reason", and reveals that he is not sure if he is up to leading the expedition. Sheppard smiles and shakes his hand, where he welcomes him to the Pegasus Galaxy.

Notable Quotes
The team discuss Kanaan and the former Hybrids Teyla: Many have already completed the treatment. They're wondering when they might be released. Woolsey: Let's not get ahead of ourselves. Teyla: These people are victims, Mr. Woolsey. Woolsey: Maybe so, but until very recently they were also enemy combatants. McKay: Fine. Well, then, we'll just keep them there forever.

Sheppard: You're not sending him back, huh? Woolsey: He is the closest thing to an expert we have. Sheppard: That's not exactly by the book. Woolsey: Don't get used to it.

Woolsey: Before I came down here, I was on a call with my superiors back on Earth. They were going over my preliminary report. Sheppard: What'd you tell 'em? Woolsey: The truth: that in my first three days as commander I violated at least half a dozen basic security protocols. Sheppard: That many, huh?! Woolsey: I let Beckett run the investigation, in spite of his condition and the fact that he's technically no longer a member of this expedition. Sheppard: Hmm. Woolsey: I sent Ronon to deliver the antidote, even though he was infected. I compromised the safety of this base to rescue someone who may well have been beyond our help anyway. Sheppard: But she wasn't, and we got her out, and if you had played by the rules, she'd be dead right now. Woolsey: The IOA would seem to agree with you. Apparently they're willing to let the matter drop. Sheppard: So what's the problem? Woolsey: The rules are there for a reason, Colonel. If I can't trust them, then I'm not sure I can do this job. Sheppard: (smiles and offers to shakes his hand) Welcome to the Pegasus Galaxy.