Welcome back to the Stargate Atlantis rewatch! We are rolling right along with season two. Today's episode is "The Intruder." Be ye fairly warned: Here there be spoilers!
The episode opens with a lovely shot of the Daedalus traveling through hyperspace and then moves to the interior of the ship to show Elizabeth alone in the mess, mulling over a cup of coffee and staring out the window (viewport?). Sheppard ambles in and they begin to converse. We learn that they are headed back to the Pegasus galaxy from a visit to Earth and that Sheppard is newly promoted from Major to Lieutenant Colonel.
(Huzzah! It will no longer be really bizarre to keep hearing everyone call him "Major" again. Equilibrium restored.)
Elizabeth and Sheppard discuss the fact that it is very convenient to be able to just step through the stargate on Atlantis and be in Earth, but extremely inconvenient to have to spend eighteen days cooped up aboard the Daedalus for the return trip (the three day trip from their first journey was due to having the ZPM integrated into the ship's systems, as that is no longer the case, eighteen days is now the rule). They also discuss that as much as they wanted to go back to Earth, once they got there, they really just wanted to get back to Atlantis. Like it or not, the city is home to them now.
They are interrupted by an airman who was sent to inform them that they are needed. There has been an accident of some sort. One of the scientists (they are returning with a new contingent to supplement their losses and expand the expedition) has been found dead. Doctor Monroe appears to have been electrocuted while working on a diagnostic of the ship's systems. Rodney and Caldwell are both dubious about this as the cause, however, since the circuits Monroe was working on didn't have nearly enough juice to render a fatal shock. They pull up the video surveillance from the time of the accident only to find that there was interference with the feed during the incident. They are unable to see what actually happened.
Rodney suggests to Caldwell that they drop out of hyperspace so they can run further diagnostics and make sure there isn't a problem with the ship's systems. Caldwell refuses, however, stating that they have just crossed into the Pegasus galaxy and stopping now would leave them exposed to an attack should any Wraith be lurking nearby. Elizabeth questions his decision and Caldwell gets angry, pulling her aside to tell him that whatever the chain of command on Atlantis, on the Daedalus he is the one that makes the calls. If she has a problem with that she needs to take it up with him privately, rather than undermine him in front of the crew. He has a job to do. She retorts yes, but not the one he wanted.
Flash back to Earth, and Elizabeth is in a meeting with Caldwell and General Landry of the SGC, along with several other important-looking military men. They are informing her that they don't think Sheppard should return to Atlantis because they doubt that after being in command for so long he'll be able to just roll over and take orders from a new commander. Elizabeth balks at this stating that Sheppard is the military commander of Atlantis. They indicate that they plan for Caldwell to take over the military aspect of the expedition as it is too important to leave under the command of a mere Major. Elizabeth tells them that Sheppard will remain the commander, reminding them that she has the full backing of the president and the IOA (the International Oversight Agency, that regulates the budget and decisions regarding the expedition and the stargate program at large). She tells them they don't want to fight her on this one and suggests that if Sheppard's rank isn't sufficient for them, they had better just promote him then.
In the present Rodney tracks down Caldwell and tells him that further research shows that the video feed went out just before the short that killed Monroe, suggesting that the two malfunctions were not random. He thinks there might be something seriously wrong with the ship. Caldwell agrees at that point to drop out of hyperspace so that checks can be run on all of the systems. McKay works with Hermiod, the Asgard stationed on board, to try to find out what's wrong with the ship. They have a fun snarky back and forth with each other, as each believes himself the most intelligent being in the room. Sheppard pops up and is creeped out by Hermiod, unused to actually working with aliens at this point.
Rodney and another scientist, Lingstrom, head out to check something out near an airlock and there is another "accident." Lingstrom had found some malicious code and was trying to tell Rodney about it when he was vented out of said airlock. Now suspecting that there may be a saboteur on the ship, Rodney, Sheppard, and Elizabeth discuss the possibilities. They quickly rule out a Wraith hiding on the ship since it underwent a pretty thorough decontamination back on Earth. Caldwell asks if any of the new expedition members have the ability to cause what's been happening and Rodney replies that all of them do--that's what comes of hiring a bunch of geniuses. Elizabeth doesn't believe any of her people could be responsible, but Caldwell orders that all civilian passengers (except for Rodney and Elizabeth) be confined to quarters anyway. He tells her that he can't trust any of them since he had nothing to do with their selection.
Flash back to Earth again. This time Elizabeth and Carson are at the SGC going over potential candidates for new medical staff. Carson gives Elizabeth a "short" list and asks for her to make the final choices. She is surprised at a name missing from the list, her boyfriend Simon. Carson tells her that Simon had refused to sign the one year-commitment waiver required to be considered, even though he already knew what the expedition was about. She goes to see him and he prevaricates, telling her she can't expect him to just give up his life and his work on such short notice to run off to another galaxy. She stares at him disbelievingly.
Back in the present again, Hermiod has located a virus in the ship's systems and it is spreading rapidly. Rodney, on a hunch, runs it through a translation program and is appalled to find out that the virus is Wraith in origin. They realize that it must have been picked up on the way back to Earth, but since it was highly compressed, it took a while for it to really get into the systems. Then it remained dormant until the ship was back in the Pegasus galaxy, close enough to the Wraith to be of use. Rodney determines that the virus is a sort of AI, ultimately designed to take over the ship's navigation and fly it into the hands of the Wraith, who could then use it to reverse-engineer their own intergalactic ships as well as to learn the exact coordinates of Earth. The AI is also programmed to protect itself from discovery and destruction, hence the dead scientists.
Once the virus is discovered, it amps up its progress. It also starts broadcasting a distress beacon designed to give away the ship's location to any Wraith in the area. Rodney thinks that rebooting all of the ship's systems should shut down and wipe out the virus, but because the Daedalus doesn't exactly have a "reset" switch, it will take him at least an hour to have everything ready to try this. Sheppard knows they don't have that kind of time so he convinces Caldwell to let him take one of the ship's F-302s (the space-capable fighter jets carried by the Daedalus) and shoot down the transmitter array to cut off the broadcast.
While Sheppard's idea does manage to shut down the distress beacon, it backfires on him in a major way. The F-302s' navigation computers share a network with the Daedalus, meaning the smaller ships have also been infected by the virus. Sheppard is unable to return to the Daedalus after shooting down the array. They decide to beam him out of the F-302, but there is a small snag. The Asgard sensors they use to lock on to beaming targets was in the array Sheppard shot down, so they have to do it "old school" and cross their fingers, hoping it works. They tell Sheppard to hang on while they make some adjustments and he waits anxiously for rescue.
Flash back to Earth again. Sheppard has gone to visit Ford's cousin to tell her that the Lieutenant is missing. She thanks him for coming in person and tells him that Ford spoke highly of him in the video message he sent back. But then she wonders if she shouldn't just tell her grandparents that Ford is dead so they don't have to worry about him being missing and maybe never coming back. Sheppard tells her he's not ready to give up yet and he will keep looking.
Sheppard is beamed back onto the Daedalus safely and Rodney and Hermiod execute their shutdown of the ship's systems. The ship goes dark.
Flash back once more. Elizabeth is at her home setting a table for a fancy dinner for herself and Simon. She wants to make one last ditch effort to convince him to come to Pegasus galaxy with her. He tells her that he is not going. She's been gone a long time, and she has always been the adventurer, not him. Then he tells her there is another thing. He has met someone else, moved on with his life. Elizabeth extinguishes the candles, knowing that it is over between them.
On the Daedalus the shutdown seems to have worked. Everyone breathes a sigh of relief and Caldwell orders navigation to get them out of there before anyone comes to investigate the source of the beacon. Hyperspace systems are still down, will take a bit to come back online, but sublight engines are working just fine. Unfortunately, as soon as they start moving the ship veers sharply off course. The virus is back and now has complete control of navigation and many of the ship's other systems. It has plotted a course for the coronasphere of the nearest star. They realize this is meant to fry them with the radiation of the star, killing them while leaving the ship intact for the Wraith.
Everyone looks at Rodney for answers, wanting to know why the shut down didn't work. He says it should have, they must have missed something. Then he recalls a similar incident at the SGC several years ago where a virus-like entity hid in a MALP to avoid being destroyed by a shutdown of the base. He surmises that the virus must have hidden in the F-302s' computers during the shutdown, then seized control as soon as the systems were back online again. Sheppard and Rodney make their way to the F-302 bay, intending to remove all of the memory boxes from the fighters so that another restart can be attempted. They arrive at the bay only to find the doors sealed tight. The virus is trying to prevent them from executing their plan.
Hermiod manages to recalibrate the beaming technology to move the two into the bay. As soon as they get in there though, the outer doors start to open, beginning the process of venting the bay to space. Hermiod manages to get the bay door's shields up in time, however, keeping the atmosphere inside the bay. He tells Sheppard and Rodney to hurry with their task though, because he does not think he can keep control of the shield away from the virus for long. They race to the fighters, removing the boxes as quickly as they can. Just as the virus brings down the shield, they make it to the last fighter and climb inside, using its enclosed life support to survive.
The ship is getting closer and closer to the star and radiation levels are rising rapidly. Hermiod tries another shutdown of the system but it is no go. They have control momentarily but then the virus takes over again. (There is much cursing from the Asgard gallery.) Sheppard realizes they didn't get all of the F-302 computers--there is still one on the ship he flew to take out the array. He fires up the F-302 he and Rodney are in, intending to shoot it down. There is a spectacular aerial sequence with the two fighters trying to best each other, but in the end, Sheppard wins and shoots down the rogue ship.
A final shutdown and reboot proves successful and they set course back for Atlantis. They arrive to find all is quiet in the city. Teyla has been left in charge, along with Zelenka, who has been having a field day with all of the new systems that have come online since the installation of the ZPM. There has been no sign of the Wraith since they faked the destruction of the city. Neither, Teyla informs Sheppard, has there been any sigh of Ford. Now that he is home safe and sound, Rodney starts to go into hypochondriac mode, freaking out about all of the radiation he was exposed to, and Elizabeth looks around, declaring herself ready to get back to work.
Yeesh. These last several episodes have all just had so much going on. I have got to get better about summing up! But. Thoughts.
"The Intruder" wraps up what I like to think of as the "interlude" episodes of this season. "The Siege Part 3" closed out all of the season one story lines and gave us an idea of where season two was headed. This episode continues in this, showing us the changes we can expect now that Atlantis is in regular contact with Earth. One of the biggest of those changes, I think, is getting used to being back under the thumb of the IOA and the SGC. The expedition had an entire year where they didn't have to answer to anyone else, and now that is most definitely no longer the case. The change will definitely take some adjusting. But I do like how Elizabeth sticks her guns about keeping her original command staff intact. She's not willing to risk her people's lives on noobs who don't get how things work in the Pegasus galaxy. Good for her.
Also, it was amusing when Rodney hung a lantern on the fact that the basic idea for this story was sort of a rehash of an earlier SG-1 episode (season four's "Entity"). One thing I will say for Stargate Atlantis is that it did a pretty decent job of taking basic ideas from things we saw in SG-1 and putting a new, and very Atlantis, spin on them. This is the first of a few examples, and I found it very well done.
Another thing that was well done was the integration of the flashbacks from the visit to Earth. They got across a wealth of information in just a few very powerful moments. Setting an entire episode on Earth, or even a chunk of this one, would have felt clunky and very un-Atlantis-like. I appreciate how they worked around that problem, and how the cuts between the present and the past really did feel very much like Elizabeth and John's memories triggered by what was going on at the moment, rather than just wedged in exposition.
I will say that I love Hermiod. If I had been given my say, he would have been made a full-time member of Atlantis. But alas, it was not to be. I get that the Asgard must be used sparingly, but I think I would pay good money to see a spin-off series about that race. The mythology the franchise built around them is just fascinating to me. It also didn't help that Joe Flanigan, who played Sheppard, was in reality actually really creeped out by the Asgard puppets. He lobbied for them to be used as little as possible on the show, and for Sheppard to have no contact with them at all whenever possible. Boo.
That's about all I have on this one, really. For me season two doesn't really kick off until the next episode, but when it does, man, it just doesn't stop running, let me tell you that.
"Is he supposed to be naked like that?" (Sheppard, about Hermiod)
"Oh crap." (Rodney)
"What did you do?" (Hermiod)
"I just ran it through a translation program. It's Wraith." (Rodney)
"Crap indeed." (Hermiod)
"Are you alright?" (Elizabeth)
"Yeah. Two arms, ten fingers...I'll check the rest later." (Sheppard)
"We should really really be dead now." (Rodney)
"I don't feel dead." (Sheppard)
That does it for this week folks. Join me next Monday for "Runner," when things really start to get interesting.