http://tvtropes.org/pmwiki/pmwiki.php/WMG/ScoobyDooMeetsTheBooBrothers

Shaggy's uncle was Civil War-reenactor and not actually from that era in time

Baring how time passes in Scooby and in HB in general, might it also be possible there was some extra time between Beauregard's death and the reading of his will? Especially given his grave didn't look new and had a bust headstone on it. Those can take time in comparison to a normal headstone.

The Sheriff says that no one's living in the mansion "now that the colonel's passed on", but given he's forgetting Farquard there we might not take him to be telling the truth there. As Sadie-Mae clearly expects to at least run into Farquard when she came over before meeting Shaggy. You don't go to a house to borrow molasses if nobody lived there. Might we assume Farquard has spent some time alone there maybe even looking for the treasure while the lawyer read the will and wrote to Shaggy?

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This theory just makes the most sense.

Shaggy's Uncle owned Great Grandpa Scooby

In the previous Scooby series we learn Scooby's Great Grandpa was a ghost and had served in the civil war. Just like Shaggy's Uncle Beauregard. Perhaps the reason Uncle Beauregard left his mansion to Shaggy is that he knew Shaggy loved his Scooby as he much as he loved his in life.

The Boo Brother's died in a house fire

Does orphan just mean they were without their parents? Given they sure do have a lot of other relatives.

I interpret orphan in this case means "without a home". They do have a lot of family but no family home to haunt. The idea that they used to have one and it's gone now makes sense, and a fire would be one of the ways that house might not be around anymore. Although I suppose it speaks to that the Boo Brothers aren't so popular given all those relatives don't want to invite them to haunt their houses. Ain't Cousin Zeko got some spare room?

The Boo Brothers do make mention they have no mother or father. Are we supposed to assume that means they aren't ghosts or that they were orphans before they died? Given they all so many relatives that are ghosts, the latter seems unlikely. Or were they disowned by their parents?

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They are orphan ghosts without a house of their own to haunt. It would make sense if their own house burned down.

There were two skull ghosts

This is likely given in some scenes the skull ghost is clearly just a man in a black bodysuit. In other cases there is nothing but bones. They do also casually drop the notion "the sheriff could impersonate all the ghosts". Or perhaps he just adjusted the costume some after the first time. Cartoon logic aside how does one adjust a costume to appear you are a skinny skeleton when you are a fat guy? The skeleton does look fat in certain scenes, factoring in the bodysuit, and other times a corset may have been used like in Scooby-Doo! Stage Fright.



I noticed that the skull ghost that the gang met on the roof is different than the one at the end. They have different voices.

The poor old witch was the boo brother's mother

And now she wants to ditch them? Well maybe given they were orphans.

Farquard was an accomplice

It's likely Farquard was looking for the treasure on his own as hinted at in the above guess. Whether he was ever aligned with the sheriff though isn't really addressed.

Farquard having the necklace that was stolen in the attic presumably means he was dressed up as that ghost, but the ghost in the attic had an accent that sounded very similar to Beauregard's ghost. It's possible the ghost in the attic was Buzby after all, but that Farquard ran into him as he ducked out of the passageway and he bribed him to keep quiet with the necklace or pretended to have simply found it.

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He was helping the sheriff. The ghost in the attic was him in disguise.In the end he betrays the sheriff and makes sure only he gets blamed.

Beaureguards ghost was real

the sheriff

AT the beginning he throws the weapon at them. He later appears in the bedroom and vanishes into thin air. At the end he appears watching them. None of these could have beendressed up as him.

The ghost ape really does haunt the mansion

Similar to the skull ghost theory above, there are two apes the escaped circus ape and the ghost ape.

There is a spiritual portal near the mansion

It would explain all the weird unexamined spiritual activities like pants moving, footsteps, Scooby being scratched and all the other unexplained phenomena.

That wasn't the circus ape

It looks just like the ghost ape. It's likely that the circus ape never made it to the mansion or maybe never even existed and the dispatcher was using it as a diversion.

one of the Scroggins and one of the Beuareguards had an illegitimate child

Yeah and Sadie-Mae is trying to repeat things all over again.

It would definitely cause a feud.

The mansion was a shelter during the war

It would explain all of the weird paranormal activity that goes on there.

The Colonel really was a Civil War veteran, but the movie takes place in the 1940's or 1950's, well before the time it was made

It would fit with a lot of the films content (old-fashioned telephone, etc.) although it would make it hard to explain Shaggy's truck (apparently a 1986 Suzuki Samurai).

Billy Bob recognizes that Sheriff Buzby was an imposter

and that was why he ignored his warnings and kept on shooting

After the events of the movie, the bear moved

Too much weird stuff going on in this town, the bear packed it up and moved to Jellystone.