After Valentine's death, both of Shadowhunters and Downworlders want to return to their normal, Jace is the only one who know about this wish, Alec presses on Jace to know about what is hidden. Also we see a great demon imposing his control on the institute which make more troubles between shadowhunters and warlocks.
There seems to be trouble brewing from every angle for the Shadowhunters in the coming future. With the end in sight, things are likely to only get worse before they come to a (hopefully) satisfying conclusion.