There are a couple of mirror images of the pilot episode, both of which I think are intentional. The first is that the first scene of this episode begins with and involves an incident on a plane which ends up crashing as a result. During this first scene, there is a man who looks a lot like Miles from LOST, but I can't tell whether or not it's him. Anyway, I'm not really sure what is going on with Marshall Bowman (whose name, by the way, is the first Aliasshout-out in the episode, since it is a combination of the eventually married characters Marshall Flinkman and Carrie Bowman). Does he conduct the test in the bathroom to see if he was infected? Why was he infected? Did the dealers know that he and Daniel Hicks (and probably John Scott, as well) were NSA and were getting too close to catching Conrad? Bowman tells the flight attendants that he doesn't have the time or the permission to explain what's happening to him. I understand why he doesn't have the time, but what does he mean when he says that he doesn't have the permission? Does he not have permission because of his involvement in a Black Ops Division of the NSA? The flight attendants most likely assume that he is on some sort of drugs, just as a side-note, and the main reason that I say that is that the flight attendant calls someone for assistance and says that Bowman wants drugs but "seems to be on something already." I mean, I probably would have assumed that he was on drugs, as well. The second reflection of the pilot episode, anyway, is, of course, Olivia's return to the tank. It's not her first time back in the tank since the pilot episode (that would be episode 1.09, "The Dreamscape"), but I still think that it is a deliberate reflection of the pilot episode.
Speaking of the tank, though, the last time that Olivia spoke to Walter about going back into the tank, he refused, saying that it was too dangerous, so I wonder what convinced him this time to allow her to go back into the tank. We don't see, because the scene cuts from Olivia telling Peter to tell Walter to prep the tank to Olivia actually getting into the tank, so I don't know. During this extended sequence (which reminds me very much of Alias), we, of course, discover that John Scott is not who we have been led to believe, that he was actually a member of a Black Ops Division of the NSA. Now, I have two thoughts regarding this revelation. The first is that in the pilot episode, Scott suffocates Richard Steig to death near the end of the episode, and the second is that, also in the pilot episode, Scott tries to kill Olivia by forcing her vehicle off the road. As far as the first thought is concerned, I have two possible explanations. The first explanation that I have to offer is that perhaps, not even his good intentions, as secret as they may have been, could have stopped him from exacting revenge. The second explanation that I have to offer is that maybe, it was an NSA "mission" to kill him. As far as why he tried to kill Olivia, though, the only explanation of which I can think is that he was being careful, pretending to kill her so as not to blow his cover but intentionally not succeeding. It really annoys me that Olivia doesn't ask him about this, but I can't allow myself to see it as a plot-hole.
After Olivia is pulled out of the tank due to her vitals spiking, she clutches onto Peter and says his name, which I find so adorable. This is definitely a scene for Olivers, as is Peter's consistent concern for Olivia. He doesn't want Olivia to trust what John tells her in her consciousness, because he is afraid that it will get her killed. I think, though, that he also secretly wants Olivia to forget about John and move on so that maybe, there will be a future between the two of them. He says to her, "What if he's still lying to you? Have you considered that?" He is so protective of her, and that is probably the primary reason why I am such an Oliver. Peternever lets Olivia down; he is always there for her, and when (thanks to Astrid convincing her, resulting in Astrid smiling in a suspiciously sinister manner) Olivia decides to trust what Scott tells her in her consciousness, he does not appear to be very happy about it. I really like the relationship between Olivia and Charlie, too, even though I really only see it as a friendship (I was never much of a Cholivia, especially after seeing in episode 1.16, "Unleashed," that Charlie was married). In this episode, it is once again made clear that they have a very trusting relationship with one another. She definitely wouldn't tell just anyone about her shared consciousness with John Scott, but she eventually comes around and tells him, because she knows that she can trust him (Charlie, by the way, is the one who notes that there were 147 passengers on the plane, the number "forty-seven" serving as another shout-out to Alias).
The Alias shout-outs don't stop there, either. Olivia and Peter go undercover in order to apprehend the dealers, using fake names, and Olivia even styles her hair differently than she normally does; this is something that Sydney and Vaughn (or whoever happens to be on the mission with Sydney at the time, but in the later seasons, it is usually Vaughn) do in just about every single episode of Alias. Also, it is agreed that the signal that Olivia will give if she needs the team to storm in is the word "Christmas," and I definitely think that this is an Alias nod, in reference to Project: Christmas, a series of tests conducted on children with a striking similarity to the Cortexiphan trials. I think that those are all of the Alias shout-outs, though, at least all of the ones that I caught, so moving on, I want to talk a little bit about Nina, since she does make an appearance in this episode (I love it when she does). When Broyles and Olivia go to Massive Dynamic so that Olivia can see that Scott is in a suspended state (a first step toward closure to which she finally comes at the very end of the episode), Nina says to Olivia, "For what it's worth, it was not mydecision to keep this from you," putting a little bit of an extra emphasis on the word "my," so I wonder whose decision it was. If Broyles knew about this, which he did, then why didn't he tell Olivia? Perhaps, it was he who decided not to tell Olivia, but why? Anyway, Walter unfortunately doesn't have a whole lot of Walterisms to offer in this episode, but while he's watching Olivia and Charlie interrogate Hicks through the one-way mirror, he says, "This is wonderful, don't you agree? It's just like a good detective movie!" I absolutely love that line.
Broyles tells Olivia near the end of the episode that despite the success of the case, Scott's status as a traitor to his country will remain the same, since there is no proof to indicate otherwise, and that kind of gets me thinking about what Scott says before he dies in the pilot episode. He tells Olivia to "ask yourself why Broyles sent you to the storage facility." Did we ever get a definitive answer as to what Scott meant? I don't think we have, and it makes me suspect Broyles of foul deeds, because what if Broyles somehow knew that sending the two of them to the storage facility would, in the end, blow Scott's cover? What if, for some reason, he was trying to take Scott out? I know that it's far-fetched but it's something to think about, because I still don't know what Scott meant when he said that. Also, Walter says that the drugs that he administered to Hinks cured him, which, as he says, is more than he can say for his own concoction. This makes me wonder if he takes certain drugs in hopes of curing himself of his insanity? I've never heard of drugs curing insanity, especially not the kind that Walter does, but I'm wondering if, in his mind, he'll one day wake up completely cured of what St. Claire's did to him as a result of his recreational drug use (which I suppose isn't really recreational if he does indeed hold this belief). Then, after Olivia asks to go back into the tank one final time so that she can say what she needs to say to John (a request that is, once again, granted), Walter tells Olivia that her mind is finally succeeding in purging itself of Scott, and I wonder how he knows this, what evidence he has. Anyway, the scene between Olivia and Scott near the water is so sad and so sweet, and Olivia needed that closure so that she could move on; we all did. Anyway, stay on the fringe.