|Atlantis Season 5|
While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by a foe he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.
Lt. Colonel John Sheppard is accompanying a botanical survey team (with a very attractive female botanist) on a routine overnight survey mission. As the scientists study a local plant, he returns to the puddlejumper to set up gear for the night when he is stunned and abducted. He regains consciousness, finding himself in a forest on the mainland of Atlantis's new home planet, to which the city was relocated a year and a half earlier. His hands and feet are bound, and Sheppard shuffles himself toward a sharp rock to try and free himself from his bonds.
Back in the city, Teyla is worried that Richard Woolsey may be lonely since he always eats alone, often in his quarters. She invites him to sit at the table with her, Ronon, and McKay, but Woolsey says he'll just breakfast in his quarters, he is working on a report for the IOA who want to review his performance as head of the Atlantis mission. Teyla says he has been a fine Commander, but Woolsey admits to feeling a little nervous.
On his way back to his rooms, he encounters a new member of the expedition in the transporter chamber. She introduces herself as Dr. Vanessa Conrad, a scientist who has recently arrived on the Apollo. Woolsey is immediately smitten. Soon, the two are on a first name basis.
Woolsey then goes to meet the IOA representative who has just beamed down from the Apollo. It is Shen. She informs him that she won't need his report: the IOA has decided to recall him to Earth and put him in charge of a new environmental impact committee there.
Afterwards, Vanessa helps a dejected Woolsey realize the IOA may be leaning towards replacing him, but if they'd already made a final decision, they wouldn't have sent out a representative to do an evaluation. Woolsey confronts the representative, who admits she wants the job for herself.
Meanwhile, Sheppard manages to free himself, and returns cautiously to his Puddle Jumper. He soon discovers who it is who tied him up: Acastus Kolya, the former Genii commander and torture master who he shot dead two years ago. Kolya claims he used Ancient technology to escape being killed. Now he wants Sheppard to give him an IDC code. He plans to have Atlantis open the Gate, then send in a bomb. Sheppard also overhears a walkie communication between Kolya and his troops: the Atlantis science team has escaped. Kolya tells the men to round them up.
In Atlantis, Dr. Rodney McKay is in his lab when Zalenka returns early from an offworld conference. He says several team members had an allergic reaction to a local food. Since he's back early, he's had an idea: he wants McKay's authorization to do a sweep of the ocean on the Atlantis planet, something they haven't bothered to do yet. McKay thinks it's a waste of time, but eventually agrees, expecting to find nothing interesting. However, almost immediately they find a submerged pod ship of alien design. They bring it to the city to study.
Back on the mainland, Kolya tortures Sheppard, but he will not reveal the IDC. So Kolya comes up with a new plan: they will attack the city directly using the puddlejumper. Kolya calls two of his men to hold Sheppard while he cuts off Sheppard's hand to use to activate the ship.
In the lab, they have turned on the pod and begin studying the data. McKay discovers the pod is giving off a mild radiation that covers the entire city, maybe much of the planet. Not dangerous, although it might give some people headaches. Zalenka tells McKay he is brilliant, but says he doesn't say it often because McKay is also a very difficult man to work for. McKay figures out the password to the pod.
Woolsey goes to a balcony where he likes to be alone, and finds Vanessa already there. He thanks her for her help with the IOA review, then asks her to dinner. She says yes. He says he'll come by to get her, but she says it will be easier to just meet there. He gets called away to McKay's lab. It is then revealed that Shen has been standing around the corner, listening to the conversation.
McKay explains to Woolsey that the pod is a treasure trove of information, a complete alien database. But it also contains the building blocks for the aliens themselves, a silicon based life form. The pod was intended to seed a new planet with life forms that would eventually evolve to where they could use the database left by their long deceased ancestors. Woolsey wants to know why the mission wasn't completed. McKay says he's not sure why the journey was interrupted, but the Daedalus could carry the pod to the intended destination. Woolsey tells him to copy the database, then ship the pod, but McKay explains that just accessing the full database will irreparably harm the biological samples. So they have to decide: either they take the data, or they send it on its way intact. They can't do both.
Kolya tells Sheppard that his men found and killed the two scientists. They are now finished rigging the puddlejumper and are ready to attack Atlantis. Kolya tells Sheppard he's disappointed Sheppard didn't put up more of a fight, but as he's talking to one of his men, Sheppard makes a run for it. The subordinate suggests they just leave him for now, but Kolya says no, he wants Sheppard found and killed before they leave.
In the city, Woolsey asks a staff member, Amelia to send a message to Vanessa Conrad that in light of McKay's findings they'll need to reschedule their dinner date. However, the staff member talks him there's no Vanessa Conrad listed on Atlantis. Woolsey argues with her, saying it's the same woman he was talking to on the balcony when Amelia came to tell him he was needed in McKay's lab. However, she says he was alone when she found him.
At the same time Sheppard tries to escape the men hunting for him. He catches one in a snare and takes his weapon, then uses it to shoot four more.
Woolsey goes to the infirmary. Dr. Keller can't find anything wrong, but he can see and hear Vanessa standing next to him while Keller obviously cannot. Woolsey demands an explanation. Vanessa says only Woolsey can see her. She says they need to talk privately. Keller suggests he's suffering from stress due to the IOA review, and gives him a mild relaxant. Vanessa tells Woolsey not to take the pills.
In the lab, McKay is still studying the radiation. He tells Zelenka he's just waiting for Woolsey to give the go ahead to extract the pod's database. Suddenly he tells Zelenka he's seen something like this before and appears worried.
In Woolsey's quarters, he and Vanessa are alone. He asks who--or what--she is. She says she is a physical manifestation of Woolsey's romantic ideals. She says he's not crazy, and apologizes for deceiving him. just then Shen arrives and asks who he was talking to. He says he's just been practicing a speech. She wants to know his decision about the pod. She argues for extracting the pod, saying the seed mission might not succeed. He says he hasn't made up his mind. She tells him that the information from the database would impress the IOA and probably save his job, but it's his choice. McKay bursts in and says they have to get rid of the pod--the radiation could cause mass hallucinations. Vanessa tells Woolsey it can also serve as a means of communication between two very different species. Shen tells McKay to immediately extract the data and destroy the pod, but Woolsey says he will make up his mind very shortly and has McKay wait.
In the forest, Kolya finally catches up with Sheppard, and in the ensuing struggle Sheppard falls over the edge of a cliff, hanging by his good arm. Kolya tells him this has gone on long enough, and tells him to use his other hand and pull himself up and a confused Sheppard does so as he discovers his hand has been restored. Sheppard confronts Kolya who reveals he is not really Kolya: it’s another manifestation of the pod's AI set up to distract Sheppard as he would have the best chance of stopping them if it came down to it. The AI never intended him to die, it just wanted him distracted. As Kolya explains the history of the sekkari to Sheppard, Vanessa does the same with Woolsey.
Ultimately it’s revealed that Vannesa Conrad is just a manifestation of the AI of a pod they discovered that holds the last hope for an extinct alien race, named the Sekkari, to survive. She reveals that when McKay flew the Jumper out of the Underwater Jumper bay during the plan to defeat Michael Kenmore, it woke the dormant pod up. The pod had been searching for a suitable planet for its race to populate but a malfunction caused it to end up on M35-117 which was not suitable for it. The AI had been observing the Expedition for weeks to see if they were trustworthy and took on Conrad's form to communicate with Woolsey and ask for his help.
Sheppard goes back to the real puddlejumper where the two scientists have been impatiently waiting for him. They ask where he's been, but he just tells them they're returning to Atlantis immediately.
Shen receives a secure call from Earth. Luther tells her he supports her as Woolsey's replacement, but the rest of the IOA Council does not. They're going to go with James Coolidge instead. But they're going to " reward" her with the same Environmental Initiative job she offered Woolsey when she first arrived. Angry, she gives Woolsey a glowing review in her report, and the IOA is forced to make him the permanent Commander of Atlantis. Woolsey is confused. Shen mentions the call from Earth yesterday. After she leaves, Woolsey asks Amelia about it, but Amelia says they haven't had a communication from Earth for days. Vanessa then appears to Woolsey again and admits to fooling Shen as a "going away present" for Woolsey.
Sheppard and McKay arrive with the pod on a gurney and realize Woolsey is talking to the AI. She then appears to Sheppard as well. McKay complains that after all the work he did on the pod, he should get to talk to the AI too. Woolsey orders the Apollo transport the pod to a suitable world for the alien race to start over and before it leaves, the AI, still appearing as Dr. Vanessa Conrad, shows all 3 of them the true form: an alien, however still very much humanoid. Woolsey wishes her luck with her mission.
Later in the mess hall, Teyla again asks Woolsey to join them and this time he agrees. Rodney states that the only reason the AI didn't reveal itself to him was because he would have figured it out. Sheppard wonders why the device was recovered after Woolsey and himself started hallucinating, and McKay says he found it with Zelenka's help. It is then revealed that Dr. Radek Zelenka has been off world the entire time. The episode ends with Rodney saying "Son of a. . ."
Alien begonia; Almond biscotti; Ancient Technology Activation gene; Apollo; Asgard transporter; Atlantis infirmary; Atlantis living quarter; Atlantis transporter; Carson Beckett; Colonel Samantha Carter; James Coolidge; Daedalus; Dirty Rotten Scoundrels; Lt. Donovan; Ellen; International Oversight Advisory; Kangaroo Jack; Kickboxing; Major Evan Lorne; Lucius Luvin; M1B-129; M2J; Mad Money; Mess hall; New Lantea's mainland; New Lantea's ocean; New Lantea's sun; Puddle Jumper; Planes, Trains and Automobiles; Sekkari; Sekkari artificial intelligence; Sekkari seed carrier; Silicon; South-East Pier; Elizabeth Weir; Wine; Yoo-hoo
Ronon: Sometimes when I walk past his quarters at night, I can hear him crying.
Parrish: Look at this, huh? It's a plant not unlike the Begonia eiromischa!
Sheppard: (despairingly) Oh, God. Lorne warned me about this.
McKay: Hey. What happened to your offworld foofoora? Thought you were the guest of honor at some big diplomatic dinner on M2J.
Zelenka: Yeah, I was, but the festivities ended early when three members of Lieutenant Donovan's team suffered a severe allergic reaction to something that we were served at the grand banquet.
Zelenka: Come to think of it, I think it might have been those little green berries with the purple specks on them, because my tongue did seem a little bit numb afterwards ...
McKay: Yeah, FYI, this conversation ended six seconds ago.
Zelenka: Yeah, um, anyway, on the way back I had an idea.
McKay: Well, have a little lie down. It'll pass.
(Woolsey introduces Shen Xiaoyi to the technician team)
Woolsey: Hello there, Chet.
Chuck: It's Chuck.
Woolsey: Excuse me?
Chuck: It's Chuck, sir. My name is Chuck.
Woolsey: Oh, of course! Chuck. Chet's on the late shift.
Chuck: (after Woolsey leaves, irritated) There is no Chet!
McKay: You realize it's highly unlikely you're actually gonna find anything?
Radek: Well, then I will have wasted an hour of my time and you'll be able to tell me "I told you so." If, on the other hand, I do find something, perhaps they'll name something after me for a change.
(Rodney pauses for a few seconds)
Woolsey: You poached my private spot.
Woolsey: Uh, what I meant to say is you discovered my personal little area.
Conrad: I'm sorry I made you doubt your sanity.
Woolsey: Who are you? What are you?
Conrad: I'm a physical manifestation of your subconscious romantic and sexual ideals.
Woolsey: Oh, God...
McKay: Yeah well, she caught me off guard, what did you want me to say? What would you have said?
Sheppard: Uh, "Weird."
- Several weeks have passed since Michael Kenmore infiltrated Atlantis in "The Prodigal".
- It has been nine months since the events of "The Seed", when Richard Woolsey took command of Atlantis.
- It is revealed that Commander Acastus Kolya did in fact die when Lt. Colonel John Sheppard shot him: Dr. Carson Beckett confirmed his death afterwards and the Kolya that appeared here wasn't the real one.
- This episode marks the first time the view is inside an Atlantis transporter when it is activated. The second time in the show, but the first time there is a flash seen during the transport.
- Atlantis expedition members shown by flag patches; Australia, Canada, Czech Republic, Russia, Spain, Sweden and United States of America
- The capsule and the premise of the humanoid median are very similar to the Stargate SG-1 episode "Scorched Earth", in which a large ship was sent across the Milky Way to search and terraform a planet for a Sulfur based life form, the Gadmeer, as well as all of the organisms of their homeworld and the knowledge of their race.
- It's revealed that the blonde, Swedish, female scientist that has been seen throughout the series has the given name Ellen.
- Jonathon Young returns as Dr. Parrish. Sheppard comments "Lorne warned me about this," in reference to Parrish's tendency to sound alarmed when he discovers a new plant, which he did with Major Evan Lorne in "Runner". Young is best known for his recurring role as Nikola Tesla on Amanda Tapping's Sanctuary.
- Anna Galvin (Vanessa Conrad/the Sekkari AI) previously portrayed Dr. Reya Varrick in the Stargate SG-1 episode "Collateral Damage".
- This episode marks the first time the Apollo has come to Atlantis on-screen since "Be All My Sins Remember'd" and the first time its shown to have come on a normal trip rather than a special mission. Usually the Daedalus takes on this role when a special mission is not required. The reason the Apollo took the trip is never given.
- McKay references the events of "Phantoms" when he talks about the similar energy signature they encountered on M1B-129.
- Jason Momoa (Ronon Dex) and Rachel Luttrell (Teyla Emmagan) only make appearances in the opening and ending scenes.
- During the episode, Dr McKay, Radek and Woolsey are discussing the alien device. Dr McKay suggests using the Daedalus to take it to it's intended destination. At the end of the episode, it is in fact the Apollo that does so.
- During the original appearence of Doctor Vanessa Conrad in the Atlantis transporter, she activates it to take them to Woolsey's quarters. However, Conrad is in fact a manifestation of the Sekkari artificial intelligence and cannot interact physically to hit the transporter buttons.
- At the end of the episode, Shen Xiaoyi leaves Atlantis via the Stargate rather than by being beamed aboard the Apollo (which was still in orbit after it had initially dropped her off). With the Midway station destroyed, and considering Atlantis' policy of restricting direct Stargate travel to Earth as to conserve ZPM power, it is strange that she would leave through the Stargate. It is possible, however, that an exception to this policy was made in her case due to her high ranking within the IOA.
- It could be Shen requested the gate be used; firstly, the Apollo is headed to a new planet to seed the pod, which could have taken them days out of their way on top of the standard three-week trip. And secondly, she likely wanted to get back to Earth as soon as possible to care of business with the IOA.
- Its also possible she left during a scheduled dial-out.
- GateWorld. on