"It is a long and dangerous way to the house of your father, the Sun. There are many monsters dwelling between here and there, and perhaps, when you get there, your father may not be glad to see you..."
--Joseph Campbell, Hero With a Thousand Faces, page 70
As of Home, the last time we saw John Winchester was twenty-two years ago, in the opening sequence of the Pilot. Until his world goes up in flames, he's smiling, warm, adoring of and adored by his family. The photographs Jenny finds in the lockbox reflect that image. There's the picture of John in his 20's (looking a bit Dean-like in a t-shirt, flashing a toothy grin); One of John and Mary, his arm around her, both smiling, presumably early in their marriage or just before it; all four Winchesters taken when Sam is a baby, close together and content. It's a different John Winchester than the grimmer one we've gotten to know only indirectly for eight episodes.
The reveal that Sam didn't know that it was Dean who carried him out of the house is a significant one for the brothers, but it's also an important hint about John. Dean tells Sam "You know Dad's story as well as I do" and says that if John had a theory about what killed Mary, "he kept it to himself. God knows we asked him enough times." This implies that John only talked to them about the night Mary died when they prodded him to, and when he did talk, he left out details. Why John would leave out the fact that Dean carried Sam out of the house, I'm not sure. Perhaps he rushed through the tellings because he hated to talk about it? Maybe he didn't think it was relevant to the quest? Probably it's a little of both, and it would be like him to not realize that telling this part of the story to the boys would hold meaning for them on a level that has nothing to do with the quest.
The prospect of returning to their old home in Lawrence, Kansas makes Dean more rattled than we've ever seen him. Which brings us to The Phone Call. It's a cry in the wilderness, a call for help that, as Dean himself says in the message he leaves for his father, he's not sure John will even get. The fact that he makes such a pleading call to his father, though, shows that Dean believes it might bring their father to them. Screwed up as their upbringing was, John trained his boys and was a large presence in their lives. He wasn't absent for any real length of time until now. I think Dean's faith in John is based on past experience as much as hope.
But the call also invites rage and frustration at John: if he doesn't answer his son's tear-filled message, it raises the question how thick-skinned is the man? Is the quest so much more important than his children that he'd ignore Dean's plea? But since we have evidence of John's affection for his kids, it also seems that if he could ignore such a call, whatever is keeping him away must be something awfully terrifying, and he has a very, very good reason for staying away.
In the course of Sam and Dean's investigation, we find out John co-owned an auto repair shop. John's former partner, Guenther, tells the boys that it "must be 20 years since John disappeared," which implies he didn't keep in contact with his Lawrence friends and neighbhors. He describes John as "a stubborn bastard" who "hated to lose" but "sure loved Mary" and "doted on those kids." The loving and doting part fits with the opening scenes of the Pilot and the happy photographs; the stubborn bastard who hates to lose matches more the John Winchester we've gotten to know through Sam and Dean talking about him. It's like there are many John Winchesters (there is also the John Winchester we get a glimpse of in 1x04 Phantom Traveller, a man who saves people from the forces of darkness and earns their eternal gratitude, the proud father who bragged about his prodigal son Sam.)
Guenther also gives us insight into how things were for John right after Mary's death. He says John didn't talk about what killed her at first, but then claimed that "something caused that fire and killed Mary." Guenther says he "begged him to get some help...but he just got worse and worse...started reading those strange old books...went to see this palm reader." Guenther reveals the beginnings of the evolution of the happy, content John of the photographs and the first moments of the Pilot into John the Hunter.
Sam and Dean check John's journals and find the diary entry, "I went to Missouri and I learned the truth." The psychic Missouri Mosley furthered John's evolution. As she tells the boys, "I guess you could say I drew back the curtains for him," opening his eyes to the existence of the supernatural.
Side note: in the scene at Guenther's repair shop, there's a shadowy figure working on a car in the foreground of that scene. It's too dark to tell, but the figure is bulky enough to be John. I'm not convinced it really is John, but it would be like him to spy on his kids, to watch them even if he won't show himself, so it could be him.
The reveal of John sitting on Missouri's couch at the end of Home is a shock. In part because he hasn't appeared for nine episodes, and in part because of the contrast with the John Winchester of twenty-two years ago, a contrast heightened through those happy photographs. But there he is, beard touched just bit with gray, still wearing his wedding ring, with sad sad eyes and the weight of twenty-two years weighing on his shoulders.
Missouri rages at him about why he won't "just go talk to your children." John says "I want to. You have no idea how much I want to see e'm. But I can't. Not yet. Not until I know the truth." And that's the end of the episode, so we don't learn yet his reason for staying away.
So the mysterious figure has finally appeared on screen, in the grim and cryptic flesh instead of being present only through journal entries and lattitude and longitude coordinates and a voice on a cell phone voicemail box. We know he did answer Dean's call for help, but Dean doesn't.
John's appearance is part legend materialized, part man-behind-the-curtain. It both increases the sense of him as a larger-than-life figure and reveals his vulnerabilities as well. He's controlled and taciturn, a strong presence, yet he twists the wedding ring on his hand (and keeps looking at it) and is clearly miserable.