As with most of the early episodes, John Winchester does not appear in this episode, but his presence is felt none the less. In fact, from the first scene with the boys, he is present.
Sam has been calling around trying to get a lead on their Father’s location. Dean asks him if he’s found anything yet, and Sam says he hasn’t. He’s checked the FBI missing person’s data bank and ran their Father’s license plates for traffic violations and found nothing. Dean listlessly admits that he doesn’t think their Dad wants to be found.
This is a very telling moment. We learned in Phantom Traveler that the boys have been leaving John messages, and that he hasn’t returned their calls. I think that means we can assume John is actively ignoring his children. John is wrapped up in his hunt and does not want his boys involved. So far we have seen the boys searching for him through their normal routes - mainly following leads they think he may also have followed. I think we can assume they’ve also contacted any mutual hunting associates and have checked up on all the places they’ve known their Dad to hide out. And after all that, they still haven’t found anything. Not a trail, not a clue, and not a single lead. So the idea that Sam is turning to more standard or “normal” routes of searching shows just how desperate he is becoming. John seems to have instilled in his sons a distrust for authority (as illustrated in the Pilot) so Sam going to the FBI shows a high level of desperation.
Dean then tries to distract Sam from their continuing hunt for their Dad by getting him up to speed on the possible case he’s discovered. Sam’s reaction is less than enthusiastic.
Sam: One freaked out witness doesn’t mean it’s the invisible man.
Dean: Dad would check it out.
Now, Dean could be bringing up John for a couple of reasons. No matter which reason it is, Dean’s motivation here is clear - to get Sam to go along with him. So Dean saying “Dad would check it out” could be his way of planting the idea that they may bump into him while investigating this gig. If Dean believes that this “invisible man case” is something John would check out, then it would be worth looking into if only to see if they could meet up with their Father. After all, as illustrated by Sam’s phone calls, they are running out of ideas.
Another reason could simply be Dean’s deeply ingrained duty to be his Father’s son. If a case would be good enough for John to check out, then it is good enough for Dean. Since both he and Sam hold their Father on a bit of a pedestal, Dean using his Father’s opinion as backup should be enough to get Sam on board.
During the rest of the episode, as the boys are investigating the Hookman, there is one more mention of John - during their first excursion to hunt for the Reverend Carnes down on 9 Mile Road.
Dean hands Sam a shotgun full of rocksalt.
Sam: If it is a spirit, buck shot won’t do any good.
Dean: Yeah. It’s rock salt.
Sam: Salt being a spirit deterrent.
Dean: Yup. It won’t kill ‘em, but it’ll slow ‘em down.
Sam: That’s pretty good. You and Dad think of this?
Dean: I told you. You don’t have to be a college graduate to be a genius.
Now, this is the first we’ve heard of the rock salt loads (although we‘ve seen them used before, mainly in the Pilot). The way Dean phrases his answer to Sam’s question of who came up with loads leads me to believe that it was Dean, and not John, who fashioned them. This matter still directly involves John though, since the invention of the rock salt loads took place during the time Sam was away at college. John and Dean would have been hunting on their own, each trying to pick up the slack Sam’s absence caused. What John’s reaction to the salt load idea was we don’t know, but I would assume Dean’s creative thinking and practical application of his knowledge would have met with John’s approval. This could also be an example of Dean’s ongoing attempt to win John's praise. With Sam gone, Dean probably felt that he had to be the best son he could be to try and keep his Father happy. He was showing John he was committed to their life by taking an active interest in the “how’s” of hunting.
There is a final bit that I wanted to mention, about how extremely well the boys work together in this episode. They are constantly bouncing ideas off one another and using each other to figure the case out. They are completely on the same page here. When they realize that the source of the Hookman’s power comes from his hook and that they need to destroy it, they come to the realization at the same moment and speak in unison. Later, when the Hookman is threatening Sam and Lori, Dean yells out, “Sam, drop!” and without a moment’s hesitation, Sam drops. He trusts Dean completely. And later still when they realize that Lori’s necklace is the last bit of silver they need to destroy, Dean and Sam perform a perfectly choreographed toss and switch. They don’t need words because they are thinking the exact same thing.
All of this togetherness leads me to wonder if John appreciates the team that he built. I’m sure things were different when John was with them and was the one clearly in charge. But without him there, Sam and Dean have filled in the gaps left by their Father with each other. They don’t need John to hunt - he’s trained them well enough that they can function independently from him. But the way they work together, the way they can fight as one unit is remarkable.
The episode ends with Sam and Dean continuing their search for John. Another town, another gig, another chance to reunite their family.