With the new characters that have been revealed, I think I know where this films plot is headed.

The Storm King will use his powers to cause trouble across Equestria, and Princess Celestia sends the Mane 6 to stop him. There will probably be some back story as to why Tempest Shadow's horn is broken, and she will want revenge for what happened in the past and side with the Storm King and help him destroy everything. I'm guessing that the Mane 6 need a boat at some point, and that is where they meet the Captain, and she takes them on her boat. The Storm King probably destroys the seaponies underwater kingdom by causing rip tides, etc. and they turn to the Mane 6 for help. Their boat probably gets destroyed and they get shipwrecked somewhere. This is the only place I can put Capper, because maybe once they get shipwrecked, they wash up on shore somewhere and he helps them. Eventually with the help of the seaponies Princess and Queen, the Mane 6 defeat the Storm King, and Tempest Shadow gets reformed.

This is my first blog post, so let me know what you guys think!