For the first few episodes of the new season, the eldest Byers sibling isn't doing much except getting stoned and lamenting the fact that he hasn't told Nancy he can't follow through with their college plans together.
As chaos reigns, however, he snaps right back into "big brother" mode — first trying to help Eleven when she's arrested, then working with her, Will, and Mike to warn their friends in Hawkins. The Byers crew (other than El) are too late to help with the final battle, and Jonathan reunites with Nancy in relief — although they still haven't talked about the whole college thing.