This was a few years ago but I'm desperate to find this story again. It involved Jared living in the country with Tom (he was a toddler I think) and a lot of women had died of a strange disease that was killing women only. Gen had caught the disease and there was a few flashbacks of Jared nursing her until she died. He was on his own and in touch with Jensen and then Jensen comes to visit him. Jensen stays and they fall for each other and live together with Tom.

It was the 'real' J2 and Supernatural existed but obs it was AU.

I hope someone recognises it from my ramblings!

Found in comments - thank you so much!