ORIGINAL AIR DATE: 10.19.2010
SYNDICATION AIR DATE: 10.03.2011
WRITTEN BY: Carl Binder
DIRECTED BY: Robert Carlyle
GUEST STARS: Reiko Aylesworth (Sharon Walker), Louise Lombard (Gloria Rush), Peter Kelamis (Adam Brody), Julia Benson (2nd Lt. Vanessa James), Patrick Gilmore (Dale Volker), Jennifer Spence (Lisa Park), Mark Burgess (Franklin), Alisen Down (Dr. Brightman), Robert Knepper (Simeon), Mike Dopud (Varro), Glynis Davies (Maryann Wallace), Leanne Adachi (Cpl. Barnes), Colin Bremner (Airman Tracy), Haley Beauchamp (Female Airman), Primo Allon (Koz)
Eli Wallace finds Chloe Armstrong studying a control console. She snaps out of what appears to be a trance-like state, and doesn't remember how she got there. As Eli chatters on, she abruptly leaves. He finds her boyfriend, Lt. Matthew Scott, in the Mess. They discuss her oddly quiet, withdrawn demeanor and the miraculous healing of her gunshot wounds ("Intervention"). Colonel Everett Young interrupts. Eli's mother has been hospitalized with H.I.V.-related pneumonia and depression.
Swapping bodies with Airman Tracy using the Ancient communication stones, Eli introduces himself to his mother, Maryann Wallace, as a "friend" of Eli's. He attempts to convey how significant Eli's top-secret work is, how much Eli misses her. She dismisses him, noting she isn't important enough for Eli to call or visit in person.
Camille Wray also visits home. As she catches up with her partner, Sharon Walker, Wray notices how much Sharon is drinking now.
Meanwhile, on Destiny, Dr. Nicholas Rush is on the Bridge, trying to manipulate the ship's countdown clock. He drops the ship from F.T.L. flight. He looks to the clock display, and expresses his frustration that he isn't getting the desired results. Dr. Franklin appears to him again, telling Rush that controlling the clock isn't easy – there are a lot of variables involved. In the Control Interface Room, Dr. Lisa Park and Adam Brody dutifully inform Rush by radio that Destiny has again dropped out without proximity to any Stargates.
As Matt and Chloe lie awake in bed, Matt asks her where their relationship is at, confessing that he is afraid of doing something to ruin what they have. Chloe attempts to reassure him, even as she turns inward.
As Colonel Young listens to MSgt. Ronald Greer complain about the Lucian Alliance prisoners being allowed out into the ship's general population, Lt. Vanessa James opens the prisoner hold. Each prisoner is assigned a guard to escort them. Scott interrupts them with news that Chloe is missing.
Trouble begins immediately as Simeon enters the Mess and whispers something offensive into Park's ear. She is shocked, and Dr. Dale Volker and Brody leap to her defense, Volker demanding an apology. Lt. James, who has been talking to Tamara Johansen, tries to calm everyone. Greer pins Simeon to the wall and sends him back to confinement, even as he instructs Destiny's personnel to search for Chloe.
Some time after Destiny jumps back to F.T.L. flight, James and her search team locate Chloe in a dark storage room, trying to open a locked case. Again, she has no idea why she is there. As T.J. examines her, Lt. Scott indicates that these blackouts are not new. Leaving Chloe in the Infirmary, Scott returns to their quarters.
Reluctantly, he opens Chloe's personal diary to find a progression from pages with recognizable writing to pages full of Ancient letters mixed with the script he recalls from the blue aliens' downed ship ("Lost"). He shows the diary to Young, Rush and T.J. As far as their limited equipment can tell them she is free of any implanted technology, leading Rush to speculate that she may be changing on a cellular level, the result of some sort of genetic manipulation. He suggests supervised freedom for Chloe might help them understand what the aliens are doing to Chloe, rather than simply confining her and learning nothing.
In addition to Chloe, Young must deal with Simeon. Accepting the man's promise to behave, Young restores his conditional freedom. Varro also confronts Simeon, who is surprised that all the others Alliance prisoners have actually been truthful about information shared with Homeworld Command. He's been lying. Varro tells him to fall in line, and start working on fitting in on board Destiny.
Back on Earth, Eli tries to explain the Stargate program, Destiny, and the stones' body trading to his mother. He tells her that even though he looks like someone else, he is Eli. She turns away in disbelief and despair. He is afraid she's giving up on life. He calls Wray who has similar concerns about an anxious, despondent Sharon.
When Rush takes a turn supervising Chloe, he leads her to a corridor he calls his place for study. The walls are covered with papers and mathematical formulae. He lets Chloe examine the equations. She fixates on a particular set, writing down the solution even though she does not understand it. Eventually handing her back to Scott, Rush makes a beeline for the Bridge.
Destiny again drops from F.T.L. flight as Rush attempts to apply his new-found information. In the Control Interface Room, Brody and Park tell Young about how the ship is dropping out of F.T.L. at places where there are no gates to dial, and then altering its course. Coincidentally, whenever this happens Rush does not answer his radio. Certain that Rush is behind this, Young confronts him when he ambles in. With seeming reluctance, Rush takes them to his study corridor, showing them the equation Chloe solved. He believes the aliens who attempted to take over Destiny ("Space") are studying them and the ship through Chloe. The others assume she is responsible for Destiny's odd behavior. Rush does not dissuade them, keeping his knowledge of the ship's bridge a secret.
Colonel Young decides to sequester Chloe. She tells Matt that she feels like she is slipping away, bit by bit. T.J. observes Chloe on the video feed, pointing out to the Colonel moments when she enters a trance and sits upright on her bed, just staring at the wall. While she may pose a risk, Young and T.J. agree that quarantine is not a long-term solution.
Camille, still on Earth, finally faces Sharon's deteriorating emotional condition. While Sharon longs for the sounds of Wray's voice, her smile, her touch, Wray tells her that these visits – no matter how short – give her the hope she needs. Imperfect as they are, their time together keeps Wray going.
Unable to persuade his mother that he is who he says he is, a panicked Eli calls Wray. Drawing on Eli's importance to Destiny, Wray uses her influence to arrange for his mom to use the stones to board Destiny herself. Mrs. Wallace awakens on the ship and stunned, but thrilled to see Eli, who shows her the Observation Deck and tells her they are doing everything they can to get home. She eventually returns to Earth with renewed hope. As she prepares to leave the hospital, Sharon introduces herself, hoping to connect with someone else in her peculiar situation.
Theorizing that the neural interface chair will kill anything alien, Rush proposes using it on Chloe. She agrees, and they run the procedure. Colonel Young and the others are convinced that it worked, and Chloe is released from her confinement. But she later visits Dr. Rush, who confirms her suspicion: she is not really cured.
Desperate for any help she can provide, Rush gambles that he can trust her to keep her condition a secret. Chloe can help his research, and she'll play along because she values her freedom. But whether she can be trusted – and how far her transformation will continue to progress – remains to be seen.
- As the next step in gaining control over Destiny's systems, Dr. Nicholas Rush is trying to manipulate the ship's countdown clock. The last time he brought the ship out of F.T.L. manually, the countdown clock didn't even activate ("Awakening").
- Rush continues to see both Dr. Franklin and his late wife, Gloria, on Destiny's bridge. But the two are never there at the same time. Gloria's concerns seem to be with Rush himself – his motivations and the decisions he is making. Franklin, in turn, comments on the technicalities of Destiny's systems and what Rush is doing with them (in this case, attempting to manipulate the ship's countdown clock).
Based on this and Franklin's still unexplained disappearance while sitting in the control interface chair ("Sabotage"), it seems possible that Franklin is a true manifestation of the ship – while Gloria may be a manifestation of Rush's own psyche, who disappears whenever the ship's image surfaces.
- Drs. Brody and Park are noticing that Destiny is acting out of the ordinary. Not only is it stopping in systems with no Stargates in range, but the ship is banking and changing course (on at least two occasions, so far). Clearly they are going to figure out that Destiny isn't doing this on its own.
Suspicious, Brody and Park reported this to Young, along with the fact that whenever it happens Dr. Rush coincidentally cannot be reached by radio. Outside of cracking the ship's master code, Brody doesn't know how Rush could be doing this – a good hint to them that perhaps Rush has cracked the code and is now steering the ship.
- Whatever is happening to Chloe, it's a lot more than just the ability to rapidly heal ("Intervention"). She is developing an incredible insight into mathematics, and perhaps Destiny and the ship's systems. While this might be a useful thing to Rush, there is evidence that it is taking over Chloe's control of herself. She is having blackouts and is found by other members of the crew, accessing computer consoles or trying to break into storage containers in a dark room, with no memory of what she was doing or how she got there.
- Chloe has also started to write both Ancient letters and an alien script in her personal journal. Matt recognized that the symbols are the same as those they saw in the crashed ship belonging to the hostile blue alien species ("Lost") – indicating that whatever is happening to Chloe has been in the works for many months now. It was Chloe, in fact, who looked at the alien ship's computer interface and intuited how to access a map of Destiny's path through the galaxy.
It seems likely that her transformation started after Chloe was captured by the aliens ("Space"), indicating that they are responsible for it. Since they could not breach the ship's defenses with their weapons and technology, they may be using Chloe as a Trojan horse.
- Rush suggests that, though they never found any implanted technology in Chloe's body (as Rush himself had a tracking device implanted in his chest by the aliens), she may be undergoing some sort of gradual change on a cellular level, resulting from genetic manipulation. This would be virtually impossible for the human crew to detect (or stop) with the technology currently available to them.
- Scott speculates that aliens might be trading bodies with Chloe using the communication stones, which is what they still suspect happened to Lt. Vanessa James some time ago ("Sabotage"). But Colonel Young believes this is not the case, since in that case they had forgotten to reset the stones. He has checked the communication terminal and confirmed that no stones were left open and active when Chloe experienced her blackouts.
- Rush has dedicated an unused corridor of the ship to scrawling mathematical equations on the walls – "a place to study, problems to be solved." One particular problem that frustrated him for months Chloe was able to solve in a minute flat.
- Colonel Young has consented to let the Lucian Alliance prisoners out into the ship's general population, though under guard and on a short leash. Varro and the others are honestly trying to fit in and prove that they can be trusted – while Simeon has been lying to Homeworld Command and just playing along. But Varro has demanded that he start cooperating, for real.
- Simeon, the more hostile of the remaining Lucian Alliance soldiers, has been giving Homeworld Command misinformation about the Alliance – and thought that Varro and the others had been doing the same. He's a bit taken aback to learn that Varro and the others are, in fact, fully cooperating and sharing true intelligence about the Alliance in the Milky Way Galaxy.
Varro, for what it's worth, has ordered him to do the same.
- When the other scientists began to suspect that Rush was causing Destiny to drop out of F.T.L., Rush took advantage of Chloe's situation to pin the blame on her. He theorized (knowing full-well that it wasn't true) that the ship's recent, erratic behavior could be caused by Chloe during one of her blackouts, or perhaps something she set up weeks ago.
- Rush says that he has improved his control over the chair interface technology in the months since he used it on himself ("Human"), which should prevent anyone who uses it from being harmed – as Dr. Franklin was, left catatonic after being the first of the crew to sit in it ("Justice").
- Rush also claims that the chair will not allow anything non-human to interface with it. This was the basis of his theory that it could cure Chloe, by effectively filtering out any non-human part of her: "There are safeguards built in that would destroy any alien lifeform that tries to use it," he suggested. But Chloe was not cured by using the chair, and it seems as though Rush knew she wouldn't be – implying that such a safeguard does not, in fact, exist.
- Nevertheless, Rush has convinced Colonel Young and the rest of the crew that he has healed Chloe of her ailment. He thinks that she can be useful in his goal of learning how to control Destiny – and that she'll keep the secret because she doesn't want Colonel Young to confine her again. But to make use of her, he may have to let her in on his secret about the ship's bridge. He'll also have to continue to monitor her closely, as she will continue to black-out and do whatever she is doing around the ship – probably with increasing frequency and intensity as her transformation continues (presuming that it is not yet complete).
- Dr. Volker leaped to Lisa Park's defense when Simeon apparently whispered something lewd in her ear, angrily demanding that he apologize to her. He may have just been defending a friend and colleague. But the intensity of Volker's response may indicate either that he has personal feelings for Lisa, or that he has a personal hatred for the Lucian Alliance and their continued presence on Destiny.
- This episode features the song "Ascolta" by Ludovico Einaudi – the piano composition that plays during the closing montage.
- The surname of Camille's partner, Sharon, is Walker.
- Chloe Armstrong is undergoing a mental transformation, making her keenly intuitive into complex mathematics, an alien language, and perhaps even Destiny herself. What started as a rapidly-healing bullet wound is now manifesting itself in far more disturbing ways. She will frequently black-out, at which point she attempts to execute a task – including accessing the ship's computer systems – and later awaken with no memory of how she got there.
Dr. Rush used the control interface chair to try and cure her (or to convince the others she was cured), but Chloe quickly realized that she is not cured. Whatever is happening to her, and however it started, is changing her on a fundamental level, so much that Chloe feels like each day she herself is slipping away a little more.
- Nicholas Rush is clearly using Chloe's changes for his own ends. He used the ship's control interface chair to convince Colonel Young, Lt. Scott, and the others that she was cured of her ailment, probably knowing all along that it was not possible. Since she proved so useful solving one of his equations, Rush intends to use her and the new insight and knowledge she has in his quest to control Destiny – and to discover the ship's purpose.
- Eli Wallace rushed home to Earth via the communication stones when he learned that his ill mother had taken a turn for the worse and been hospitalized. When it became clear that she was emotionally depressed because he had vanished from her life, unable to even call her low these many months, he decided to confess the truth about Destiny, and the fact that he was inhabiting another person's body. He even had to tell her that it's possible she may never see him again. As he expected ("Earth"), she didn't believe him – couldn't even comprehend what it was he was trying to explain. She told him that her son is all that she has left, and is the reason she is able to get up in the morning – though she didn't fully realize it until after he was gone.
With help from Wray, Eli was eventually able to welcome his mother on a visit to Destiny (again, by communication stone), and show her that everything he tried to tell her was true. She embraced her son and told her how proud of him she is. Back on Earth, she quickly recovered and was discharged from the hospital. Now Eli has the security of knowing that his mother is in good health, both physically and emotionally, and that she knows where he is and why he can't see her or call her.
- Camille Wray was able to visit her partner Sharon for the third time in about a year, but found that Sharon is growing increasingly despondent over her absence. She has started to drink more, and finds it more difficult to be the strong support she has been when Camille has visited in the past. To help support Sharon, Camille has put her in touch with someone else on Earth who is missing a family member on Destiny, Maryann Wallace.
Camille told Sharon that these trips home to see her are the only thing that is keeping her going.
- Simeon has been feeding Earth misinformation about the Lucian Alliance, and thought that his comrades had been doing the same. He told Varro that he is willing to play the game, and was somewhat shocked to hear that Varro and the others are legitimately trying to cooperate and fit in on Destiny. Simeon may feel that this is a betrayal, and have no real intention of going along with the others.
- Varro, on the other hand, has been giving Earth legitimate intel and trying to help his people fit in. They've secured release from their holding area and can now mingle with the rest of the crew. When he learned that Simeon is jeopardizing that effort, Varro chastised him severely.
- Matthew Scott is starting to wonder about his relationship with Chloe, since she has started to withdraw (due to her condition). He's never been very good at long-term relationships, and doesn't want to be responsible for doing anything to push her away or otherwise hinder their relationship.
- Are the blue aliens responsible for what is happening to Chloe? What is she doing around Destiny? Is she going to give them access to track and board the ship?
- Will Chloe keep the secret that she isn't really cured? Even from Matt?
- Will Rush reveal the bridge to Chloe? What further plans does he have for her, and does he think that she will help him control the ship?
- How much conscious control does Chloe have over the knowledge or basic insight into Destiny that she seems to possess? Can she help Rush by her own free will, or is she only of use when she falls into a trance?
- What is going on with Chloe, anyway – and how did it start? Did the blue aliens alter her or infect her with something, during her brief time as their prisoner? If so, what is their agenda?
- Will Sharon and Maryann be able to offer one another the support they need? Will they perhaps bring in other Destiny family members who have been told the truth about where their loved ones are?
- Is Simeon going to go along with Varro's plan to be honest with Earth and try to fit in on Destiny? Or will he decide to take matters into his own hands?
- Did Chloe's momentary connection to the chair's neural interface actually do anything – perhaps giving her access to the ship itself?
- Though it aired fourth, "Pathogen" was the first episode of Season Two to be filmed. It marks actor Robert Carlyle's ("Nicholas Rush") Stargate directing debut.
- What's to prevent these characters from using the bodies to commit other antisocial and illegal acts? Where's the limit? "Great question. And it's one executive producer Carl may be positing in Season Two." (Executive producer Joseph Mallozzi, in a post at his blog
- "Today, we watched the very first director's cut of the new season. Congratulations go out to writer Carl Binder, the cast and crew, and, especially, Robert Carlyle who delivered big time in his SGU directorial debut. Next up for Bobby: he'll be doing the catering for episode 7. Can't wait to try his spicy jambalaya!" (Executive producer Joseph Mallozzi, in a post at his blog)
- "We looked at the first four or five scripts that we were starting with for season two and out of all of them we felt that 'Pathogen' would be the best one for Bobby to direct. It was then moved to the front of the production schedule so that he'd be able to prep for it as opposed to trying to do that while filming another episode, which would have been very difficult. So we decided to start off the season with Bobby's episode and that was a lot of fun. It was quite a long prep as well because we started, then broke for the  Olympics here in Vancouver, then came back to work and prepped for another week or so before filming began.
"'Pathogen' originated from two stories that I wanted to do. At the end of last season, Brad Wright pitched this idea to me of what if Eli's mom Maryann – who's a nurse and who we established in Season One is HIV-positive, having accidentally gotten stuck with a needle – takes a turn for the worse because she's depressed. Eli's father left shortly after his Mom got her diagnosis, and since then all she's had is Eli. With him gone, she's lost her reason to live. When Brad pitched that idea I said, 'I love it. Can I write it?' As often happens, one of these guys will come into my office, or we'll be in the writers' room, someone will pitch an idea and if I connect with it, I'll ask, 'Can I write it?'
"So we had that story, but it wasn't a full episode. Rob Cooper had also come up with an idea for a half-season-long arc with Chloe gradually going through this change, where we find that her kidnappers – the blue aliens from Season One – did more to her than we first thought. You kind of got hints of this last year, like when she, Lt. Scott and Eli find the alien ship in 'Lost' and she's able to read alien language. Apparently Chloe has been having blackouts, during which she's been operating consoles and doing all sorts of other things that she has no memory of. We discover that something is taking her over and growing inside her brain.
"We decided, OK, let's put this story together with Eli's mom's story. Then I pitched a C-story, with Camille Wray returning home to see her lover, Sharon. We've established their relationship as the one stable, perfect relationship of all those on the show, but one of the things that intrigues me is what if you really were stuck on a ship on the other side of the universe. You can go home to visit but in someone else's body. That's going to mess up any relationship, no matter how strong it is.
"Up to this point we've seen Camille and Sharon as this positive, hopeful couple that finds strength in each other. Now, though, I wanted to portray the opposite of the episode I wrote last year called 'Life,' where we start to see these little fractures in this relationship, and at the end of the story Sharon says to Camille, 'Is this how it's going to be from now on? You coming home and showing up in someone else's body? I miss your voice, your face. I want to see you.'
"In essence there's a pathogen there, too, just like with Eli and his Mom as well as with Chloe. So the entire episode is about a pathogen in various forms, taking root and affecting our people. It has kind of a dark feel to it, and Bobby rose to the challenge and had a good time directing it. Again, it was a good way to start off the season because it wasn't really a complicated story as far as visual effects, action or stunts." (Writer and executive producer Carl Binder, in an interview with SciFiAndTvTalk)