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That is a theory I had come to a few episodes into the season and it just kept expanding and looking more and more obvious every week. I hope I'm wrong but I have a bad feeling that my guess is spot on

After hearing her parents fighting about how Ben cheated on Christy with Jess, Abby watches as Ben leaves the house and, in a stage of panic and extreme concern, waits for him to return. As Ben returns from a night out drinking with Dave, Abby hears the taxi pull up and watches him get out, only to see Ben go over to Jess' house instead of returning home. Being an extremely concerned child, she grabs a flashlight and goes across the street to see what Ben is doing there. She sees Ben putting Tom to sleep and acting fatherly towards him, and fears that Ben will leave his own family in exchange for one with Jess and Tom. As Ben leaves, Abby gets in and somehow tricks Tom into going with her to the trail where Ben takes his morning runs, where she kills Tom using the flashlight she grabbed from her garage (Ben's), knowing that Ben will see him there and, in her childish naivety, be dissuaded to leave his family because of Tom's death or because of the simple fact that she believes Jess will move from the house across the street and the Crawford's will live happily ever after.