While Sheppard goes to the mainland with two botanists, Rodney, Ronon, and Teyla have lunch and Teyla observes Woolsey eating by himself. She invites him over but he says he has to head back to his quarters to review for an IOA assessment of his performance.
On the mainland, Sheppard tries to flirt with Dr. Kiang but she's more interested plants. Parrish yells but when they rush to see what the matter is, he's only excited about discovering a new plant specimen. When Kiang would rather check out the plant than him, Sheppard heads back to the jumper. As he walks through the woods, he hears someone who stuns him with an energy blaster. He wakes up a little later and discovers he's been tied up. He starts to free himself on a sharp rock.
On the way to his quarters via transporter, Woolsey runs into a new staff scientist, Dr. Vanessa Conrad. She flirts with him and as he gets out of the transporter he turns back to talk to her but the doors close behind he can get anything out.
Sheppard gets free but discovers that his attacker has taken his gun and knife. He goes to the jumper only to discover that the same person has wrecked the interior.
Zelenka returns to Atlantis and explains to Rodney that they had to call off his diplomatic mission early when some of the soldiers were allergic to the native food at the banquet in their honor. Rodney could care less. Zelenka has an idea for scanning the ocean's bottom for temperature differentials to familiarize themselves more with their planet, but Rodney is less than thrilled. Zelenka persists and Rodney gives him the authorization to proceed. Rodney sets up the scan and they soon discover a signal.
Woolsey greets the IOA representative, Chinese Ambassador Shen Xiaoyi. He shows her around Atlantis and she informs him that he's being recalled to Earth to chair the IOA environmental committee. Woolsey isn't happy at being dismissed and Shen says that his unorthodox decisions have caused the IOA to question his judgment.
Sheppard manages to find a knife and tries to attack a soldier. However, another soldier cuts him off: Kolya, the Genii ex-Commander. The first soldier knocks Sheppard out while his back is turned.
Zelenka discovers that an alien artifact is responsible for the signal and brings it back to Atlantis for study.
Sheppard wakes up and Kolya explains that he used an Ancients force field to protect himself from death the last time they met. Thanks to some less-than-trustworthy Atlantis contacts, Kolya has discovered Atlantis' new planet and informs Sheppard he plans to destroy the city in revenge. However, he needs the IDC code to send a bomb through the Gate as the first step of his plan, and starts beating the uncooperative Sheppard for the info.
Vanessa comes to visit Woolsey in his quarters and offer him an invitation to the movies. He passes, saying he's not having a good week. He explains that he's being recalled and Vanessa points out that the fact the IOA sent Shen all the way from Earth suggests that something is up. Woolsey confronts Shen and tells her he's figured out that it's not a done deal and she's there to evaluate him. She agrees but notes that the final judgment is up to her... and she wants command of Atlantis.
As Rodney tries to decipher the alien device, Zelenka surprisingly admits that he's brilliant and that he'll figure it out. Rodney is surprised and worried, but gets to work and tries to track down a signal the device is giving off. He realizes that the signal is blanketing the city and figures that the system needs a password. He works out a program to break the device's security system.
Sheppard refuses to talk and Kolya orders two of his soldiers to report in. Kolya comes up with new plan: they'll repair the jumper and attack Atlantis with it. When Sheppard reminds him he needs someone with the Ancient gene, Kolya cuts off his left hand. As Sheppard moans in pain, Kolya asks him what he's refusing to confront.
Woolsey finds Vanessa at the balcony where he goes to think things through. He thanks her for her idea and she wonders why more people don't see him as a good man. He asks her out to dinner and she agrees, but says that she'll meet him. They're interrupted when Technician Banks comes to tell Woolsey that Rodney needs him. As Woolsey leaves, he's unaware that Shen has been watching him the entire time. Rodney briefs Woolsey on the fact he's broken the security and discovered the device is a delivery device that contains biological specimens capable of spreading a sentient life form on other planets. It also has an extensive database of information. Rodney warns that if they try to access the data, they'll destroy the specimens.
Sheppard manages to escape from Kolya, who insists on dealing with Sheppard before launching the attack on Atlantis. Sheppard picks off the Genii soldiers one by one using a series of traps.
Woolsey has Banks notify Vanessa he won't be able to make their dinner date, but she reveals that there is no Dr. Vanessa Conrad on the base. She also confirms that when she delivered Rodney's message on the balcony, Woolsey was alone. He goes to the infirmary but Dr. Keller can't find anything wrong. Vanessa appears but only Woolsey can see her. All of his efforts to talk to her just confuse Keller so he tries not to acknowledge her. He complains about hearing odd sounds and Keller gives him some pills for treatment but Vanessa suggests he shouldn't take them. Meanwhile, Rodney finally identifies the particular signal and says they're in trouble.
Woolsey finally meets with Vanessa in his quarters and asks what's going on. She explains that she's a manifestation of his romantic and sexual desires, and it's vital he listen to her. Shen comes in and say she saw him talking to himself on the balcony earlier. Woolsey tries to cover but Shen further questions his judgment and says they should ignore the biological specimens and obtain the data. Vanessa objects and Woolsey accepts her judgment, even though it's against IOA protocol and will certainly cost him his position as head of Atlantis. However, Rodney arrives and explains that the electromagnetic signal causes mass hallucinations. Woolsey gets Shen and Rodney out and turns to Vanessa for an explanation.
Kolya ambushes Sheppard, knocking him off a cliff. Sheppard dangles by his one hand, but Kolya tells him that he doesn't want him dead and he should use his other hand to pull himself up. Sheppard realizes that his left hand is whole once more and pulls himself up.
"Kolya" and "Vanessa" both simultaneously explain that an ancient race, the Sekkari, built seed carriers when their planet was threatened and sent them off throughout the Pegasus Galaxy. Each one holds biological specimens to recreate the race along with the entire history of the Sekkari. One carrier landed on Atlantis' planet two thousand years ago and went to the ocean's bottom. It remained active until it picked up an underwater jumper signal and reactivated. "Vanessa" and "Kolya" are the carrier's artificial intelligence program. Vanessa contacted Woolsey to determine if he would spare the carrier, while "Kolya" worked to distract Sheppard, who would have lead any military attack on the carrier. Vanessa apologizes to Woolsey for the deceit, while "Kolya" says that the hallucination was created from Sheppard's subconscious fears. Sheppard gets the scientists and heads back to the jumper. Vanessa informs Woolsey that he has a decision to make.
Shen receives a coded signal from Earth. The IOA contact informs her that they are going to give someone else Woolsey's job, and she'll get the environmental chair he was going to get. Shen is less than thrilled. As she leaves, she informs Woolsey that she's given him a suitable review and he'll be staying on as base commander: if she can't have the position, she won't help someone else to get it. As she leaves, Banks notes there haven't been any coded transmissions from Earth. Woolsey realizes that Vanessa is responsible and she says it's a thank-you for his help. Woolsey has decided to use the
Apollo to transport the seed carrier to its intended destination. Sheppard and Rodney arrive with the device and they wonder what will happen to Vanessa. She says that she'll "sleep" until the Sekkari race has been recreated fro the specimens. Rodney isn't happy that he can't see her, and she reveals herself to them in her true alien form before departing.
Later, the team are having lunch and this time Woolsey accepts their invitation to eat with them. Rodney is his usual superior self, saying that AI didn't try to manipulate him because he would have seen through the deception. However, Woolsey notes that Zelenka hasn't returned from his mission yet, and Rodney realizes what was directing him to bring the artifact to Atlantis...
Share this article with your friends