In the first few episodes following Jessica's death in the pilot episode, we saw a Sam who was very much a broken man. Not broken in the sense that he was helpless - clearly he was not. But a Sam who had been through a massive trauma, and, as Phantom Traveler begins, he's still putting himself back together.
Each of the early episodes shows Sam finding one more piece of himself. In Wendigo, despite his early resistance, he ultimately put himself in the front line to protect the innocents: had Dean been a touch slower with that flare, Sam might have been the wendigo's next victim, and he knew it when he put himself in the firing line. In Dead In The Water the same pattern was repeated: Sam wanted to get out of town, it was Dean who insisted they must stay and again Sam put himself in danger to save someone else. Twice, in this episode: first when he saves Andrea from drowning in her bath, and again when he jumps in the lake to save Lucas. (This is not to devalue Dean's part in both rescues - I know he's a hero too. But I'm meta-ing Sam here.)
The point I'm making is this: though in both of those episodes Sam "did the hero thing" every time he did it because he followed Dean to the place where it became necessary. If not for Dean, Sam wouldn't have been there to save any of those people: he would have been off searching for John and to hell with the civilians. Dean lead the way, Sam followed: it's probably a childhood pattern, since Sam is the younger brother and, to kids, that age difference would be a huge difference.
Phantom Traveler is the first time we catch a glimpse of Sam as a leader and, to me, this says a great deal about him. Sam is a natural leader. Once he's voluntarily committed himself to a course of action he does it, and does it extremely well. This is, I suspect, at the root of his conflict with John: Sam is too much a natural leader to be able to follow unless he's willingly accepted another's leadership, and John never gave him that choice. Sam willingly accepts Dean's leadership, but not their father's. But that's a digression and I'll save that meta for a later episode.
Our introduction to Sam in this episode is a view of a man suffering from an early stage of post-traumatic stress disorder. The insomnia and nightmares are classic symptoms. He tells Dean it's not only about Jessica's death, but being back in "the family business": he's scared. It's a small peek into how Sam must have felt about his father's choices when he was younger and I find I'm not surprised by his determination to be done with it all.
Yet, it's as if admitting that aloud, to Dean, has allowed Sam to move beyond it. Though the initial impetus in this episode still comes from Dean, more and more Sam is moving into the forefront, and Dean accepts him doing it. Their partnership is becoming one of equals. While Sam won't accept the compliment of being considered "an even trade" for his father, time and again in the episode Sam demonstrates that, in many ways that's exactly what he is. For example, when Jerry is explaining the circumstances of the plane crash to Dean and Sam, it's Sam who leaps in with the plan of action: "We're going to need passenger manifests, a list of survivors... " At which point Dean jumps in with his own suggestion: examine the wreckage. I notice that, though Dean's plan is perhaps the more direct route to answers, the brothers followed Sam's original plan first. Dean's is Plan B.
Sam is not happy about following Dean's plan, as they do later in the episode. He's okay with impersonating Homeland Security agents to interview witnesses (though even then he points out it's "pretty illegal, even for us"), but using the same ruse to get access to the plane wreckage is different. Though he goes along with Dean's plan, and even points out that they need to look the part this time, his unease is clear. I think that's why he rags on Dean's EMF meter. There's always a certain level of banter between the brothers, but in this one instance I think what Sam says is almost cruel. Dean seems to shrug it off, but he's so clearly proud of his work and Sam's "it looks like a busted up walkman" is mean (particularly as, when we get a clear view of it later in the episode, it doesn't look busted up at all).
The role reversal begins when Sam discovers that a demon is behind the plane crashes. He's done the research, reached a conclusion and is now moving into figuring out what to do about it. For the first time, Dean is more reticent. He implies that a demon is out of their (his?) league and says "I wish Dad were here." Though Sam expresses the same wish, he has become determined to fix this problem. This is the moment Sam steps up and becomes the leader.
This is also the first time we see Sam in full-on "saving people" mode. Thus far, this road trip hasn't been about that for Sam. He'll step up and save people, if there are people to be saved, but unlike Dean he doesn't seek out those opportunities. It's all about finding his father, and finding the thing that killed Jessica (and at this point no one has identified it as a demon). In Phantom Traveler, Sam's priority changes, albeit temporarily, and I wonder if it's because what they're trying to prevent is a plane crash. Though there's a supernatural cause, the reality is a plane is going to fall out of the sky. That's a very real thing, and perhaps it means more to Sam for that reason. A plane crash isn't part of Dean's world of ghosts and monsters. A plane crash is utterly real and maybe to Sam, who was in college, living in the "real world" in the post-911 years, it's far more significant than the horrors Dean has been facing.
So much so that Sam is willing to get on that plane with or without his brother. Dean's fear of flying puts Sam firmly in the position of leader for this particular mission. Sam decides they're getting on the plane. Sam orders Dean to go back for supplies. Sam selects a suitable exorcism ritual from John's diary. He's calm, he's focussed and he's very determined to get the job done.
On the plane, Sam seems to enjoy that Dean is scared. It harks back, a little, to their conversation at the beginning of the episode, with Dean's insistence that he's never afraid of the job, but I suspect it's also another little role reversal: Sam is getting a chance to, in effect, be the big brother, and he can't help enjoying it a little. But that wicked pleasure doesn't get in the way of the job for Sam. From the moment he identified that a demon is at work, Sam remains completely focussed on what they need to do. He helps Dean to deal with his fears, gets Dean focussed on the job. He does that twice, in fact: first as the plane takes off, by encouraging Dean to focus on the job at hand, and later, when Dean's (totally justified) fear of the plane crashing seems about to overwhelm him, Sam gets Dean to calm down by pointing out to him the one thing that would be far worse than that: Dean is making himself susceptible to possession. It's really great psychology and it seems to come naturally to Sam: one of the qualities that makes me see him as a natural leader. In fact, Sam demonstrates that leadership ability a third time during the exorcism itself, when he calms Amanda down enough to get her to help them while they exorcise the demon.
They're working to a tight deadline and Sam stays remarkably calm under pressure, when you consider that failure means almost certain death. He barely even flinches when the demon throws Jessica's death in his face. The demon has looked into his mind and seen Sam's most vulnerable wound, and yes, it makes Sam hesitate. But only for a fraction of a second, and then he gathers himself and completes the job.
It's only later, when it's all over, that we see how deeply the demon has shaken him. Sam has come a long way in this episode. He's shown he's capable of moving past Jessica's death and becoming the whole man he was. He's not quite there yet, but in defeating this demon he's firmly on the road to recovery.
I've emphasised Sam as leader here, but there's no question the brothers are very much a team in this episode. Though Sam offered to get on the plane alone the events leave no doubt that Sam couldn't have defeated the demon without Dean's help. And that's important too, because by the end of the episode the dynamic between them has changed subtly. The last scene of the episode is almost a mirror of the last scene of Woman In White.
In Woman In White, we saw Sam checking weapons in the trunk of the Impala before he turned to Dean and said, "We've got work to do." That "work" being find their dad, and Jessica's killer. Here, at the end of Phantom Traveler, the brothers listen, together, to their father's message, which in effect tells them they won't be finding him any time soon. And again it's Sam who moves, Sam who signals it's time to get going. But this one is silent, he just gets into the car, leaving Dean to make his own choice.
Lastly, and on a completely new tangent, I want to go right back to the beginning of the episode, because our first view of the brothers in this ep is a scene almost archetypal in slasher/horror movies. The camera pans lovingly up Dean's body. He appears to be deeply asleep. (Okay, in a seventies slasher flick Dean would be a busty blonde woman sleeping in lingerie, but bear with me - I'm making a point here.) We hear the sound of a door opening, and the camera pans upward to reveal the figure of a man, quietly entering the room. The figure is just a silhouette, behind an obscuring glass wall. The music is tense and menacing as the shadowy figure gazes down at Dean.
If this were a slasher flick, the figure behind the glass would be the bad guy and the poor person sleeping on the bed would be about to die horribly. This, of course, doesn't happen since the figure in question is Sam and Dean is no helpless victim. Still, for a moment it's quite a sinister view of Sam. It makes me wonder (see, I said I have a point) if I might look back at this episode in another season or two and see this scene as a portent of things to come.