I run a webcomic called Jack that you can find here: (http://jackimations.deviantart.com/) among other things. It stars character based on me and my friends and yeah. Shameless self promotion for the win!
My headcanons and theories that may be true but SHOULD NOT be taken as fact (I also didn't make all these up)
The Minish Legend was the first known time Demise's curse affected hyrule (hence the purple smoke and incarnations of Link and Zelda) and Demise's spirit/mailce was sealed in the bound chest.
When Vaati opened the chest Demise's Malice latched it's self onto Vaati and didn't leave until the end of Four Swords after three defeats in the body.
The Downfall timeline was the created when Link went back to the pass to the Spirit Temple in Ocarina of Time, which is the only point in the gamme where time traveling to the pass is mandatory. The Future he returns to becomes the Adult Timeline while the other futrue became the Downfall timeline because of a lack of a hero and sage of spirit.