Maybe the third episode happens some time after the end of the second. In previous moments where Sam and Max has been separated, they have pretty much reunited on the same episode and also a short perioid of time.
My guess is that episode 3 will start some days or even weeks after the disappearance of Max's Brain, so the time without his dear crazy violence-lover best little buddy has leaved him with an empty void which only Max's chaotic shenanigans used to fill. So now it's Hardcore Sam time!
I still hope we'll see Max in the episode in some way. After all, the main gameplay mechanic of the season is Max's Psychic Powers, so an episode without 'em would feel weird (also I wanna see more new toys!)