After finding out just how the co-op in Far Cry 4 will work when one player doesn't actually own the game (spoiler: It's a client), we also found out that the co-op won't include any of the single player story missions.
Taken directly from Eurogamer:
It's going to be a colossal app, since it will contain all of the game's content sans its story-based missions – which are the only content available exclusively in single-player.
Somewhat disappointing, since I was looking forward to playing through the game entirely with a buddy, but considering Far Cry 3 had a completely separate co-op option that wasn't part of the main game, at least it's a step in the right direction.