This is one of my favorite "J2 established relationship on the rocks" story. I hope you'll enjoy it.
Both Sides Now by nocturniquette Summary: Jared is Jensen's world and that world is about to be insidiously threatened. Through the nightmare, will their children and relationship be enough to see them through, or is it time to accept things will never be the same again? (Warnings- this is a fiction dealing with life threatening illness, past child abuse, and infidelity_both suspected and actual. Also, if it matters to you, bottomjared/ Top!Jensen) http://www.sinful-desire.org/archive/viewstory.php?sid=2440&warning=5
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Both Sides Now by nocturniquette
Summary: Jared is Jensen's world and that world is about to be insidiously threatened. Through the nightmare, will their children and relationship be enough to see them through, or is it time to accept things will never be the same again? (Warnings- this is a fiction dealing with life threatening illness, past child abuse, and infidelity_both suspected and actual. Also, if it matters to you, bottomjared/ Top!Jensen)
http://www.sinful-desire.org/archive/viewstory.php?sid=2440&warning=5