I think it's unlikely we'll see The Scouring of the Shire in the last box, just like we didn't see Fog on the Barrow-downs and Old Forest in Black Riders. I think, however, that we'll most likely see it as a Fellowship or Gen Con quest that you can insert into campaign mode, much like the aforementioned quests.
Aw, come on! It could fit, easily!
1. Saving Frodo
2. Sneaking through Mordor/Destroying the Ring (SPOILER ALERT: The Ring gets destroyed, just in case you haven't read the books or seen the movies)
3. Scouring of the Shire