Harry Potter caused the Calamity in an effort to remain famous

What if Isaac Newton got hit on the head by one of Weasleys' Wildfire Whizz-bangs and they had to pay for the damage done so they erased his memory and in the process accidentally made him a math genius

I know that's totally random.

Fudge hates Dumbledore because Dumbledore rejected his advances when Fudge had a crush on him

Oh god-

Dragons are secretly carrots in disguise

The department of Mysteries can create potions that can turn you head into a crystal orb

The brains in the room in DoM is Fudge's

The aurors are actually supporting Voldemort

The slight complication is that it's true.

Umbridge is actually Dobby but they shape-shift when needed!