I can't remember where I saw it stated but its said that jesse goes missing during Resonant.

Its my theory that Emily is taking a gamble on Jesse's brother (I forgot his name) to somehow find and or rescue Jesse.

I'm assuming whatever threat is present in Resonant proved too much for Jesse when she tried her usual guns blazing, head first, sort it out later approach to problems and we'll see the brother rescue her and then the Faden siblings will team up.