First off,I'm not completely sure that Ali "passed away" there's not much evidence that she did oder didn't..but I can tell Du according to Garret before his passing that he sagte Byron was there with Ali,and then the flashback in last episode when he was conversing with Ali and it went completely wrong where she tried to talk to Ella (Aria's mother) and then Byron took hold of her hand and took the phone away but I'm not completely sure,it makes some sense that he would because of their fights while conversing but I'm not sure.
Byron was desperate to keep alyson from talking about what she and aria saw in his car making out with Merideth . He warned her to back off saying she was just a child not able to understand love. She threatened back and then a rustle in a nearby busch Garet watching- made him apprehensive about his anger. this happened near the gazibo construction site. She was making his life a living hell. Garet asumed what happened after. Confession to spencer when he got her alone on train on Haloween special.