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A large part of the plot of the 1st series of Supernatural is based around Sam and Dean trying to track down John.

Why does John avoid them for so long and why does he send them to various hunts?

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up vote 3 down vote accepted

It was explained in this conversation:

Sam Winchester: But after, we're gonna meet up, right? Use the gun together, right?
Sam Winchester: You're leaving again, aren't you? You still wanna go after the demon alone? You know, I don't get you. You can't treat us like this.
John Winchester: Like what?
Sam Winchester: Like children!
John Winchester: You are my children. I'm tryin' to keep you safe.
Dean Winchester: Dad, all due respect but uh, that's a bunch of crap.
[Sam and John look at him in surprise]
John Winchester: Excuse me?
Dean Winchester: You know what Sammy and I have been huntin'. Hell, you sent us on a few huntin' trips yourself. I mean you can't be that worried about keepin' us safe.
John Winchester: It's not the same thing, Dean.
Dean Winchester: Then what is it? Why do you want us outta the big fight?
John Winchester: This demon? It's a bad sonofabitch. I can't make the same moves if I'm worried about keepin' you alive.
Dean Winchester: You mean you can't be as reckless.
John Winchester: Look. I don't expect to make it outta this fight in one piece. Your mother's death? It almost killed me. I can't watch my children die too. I won't.
Dean Winchester: What happens if you die? Dad, what happens if you die and we could've done something about it? You know I been thinkin', I think maybe Sammy's right about this one, I think we should do this together. We're stronger as a family, Dad, we just are, you know it.
John Winchester: We're runnin' outta time. You do your job and you get outta the area. That's an order.

Source: Quotes for John Winchester

So, there are basically two reasons, both closely related to his sons:

  1. His own efficiency, as they get him distracted, for he goes after a dangerous daemon (the yellow-eyed one), and thus worries about them getting killed.

  2. He is afraid to actually see them die, like he saw their mother die.

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That explains why he doesn't want them in the final fight, but I'm still struggling to understand why he is missing through all of S1 - is he hunting it all that time? – Liath Oct 1 '13 at 6:39
I always understood above as the reason for all of his absence, not just trying to keep them out of a big fight. All that time John was hunting the yellow-eyed daemon, which is "a bad sonofabitch". – Vedran Šego Oct 1 '13 at 7:27
@Liath: Yes. He's hunting it right from the start of the series. – Andrew Martin Nov 26 '14 at 10:22

The reason why Sam and Dean can't be together with John on the hunts, is because John is vulnerable when his sons are around, and that he's stronger on his own.

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