Ok here's my theory its just speculation so don't take this as the most correct theory ever.
Ok here I go. When the Darkness was created by Nox Deious he was just darkness a part of Decious, when he possesed Mario, he then left and took on his form of the most powerful host, Mario. Then later in Act 2 the Darkness got defeated and stabbed by Wario, but then Merlin reveals the only way to kill the Darkness is to use a spell that will make human as fans say but I don't.
See, the spell may have not turned the Darkness to human at all. It may have just lowered his body's vulnrebility to a human scale. So Merlin most likely ment that when the spell was chanted the Darkness would stay dead and not come back in his body instead of just saying he is now totally human.
And that's my point. See, the Darkness will not and wil never be human, he just darkness a coud of pure darkness! Nothing can change that, not even spells or new bodies, he is just darkness, therefore he can die from a 23834573734ft fall and still live as he pleases. He can be disguised by spells and bodies but that doesn't change a thing, its just a disguise.
Now at OP BlindStorm, this is where the fans get a bit whiney, they say that when the beacon is destroyed, the Darkness visited Mario, Snake, Ness, Luigi, and Wario in a spirit form and said that their powers are gone and he is gone too and leaves.
Now did anyone find that suspicisous. I don't know about you but I'm not inclned to believe the Darkness would give up that easily just when the guy's powers where gone?
My theory is that the Trifecta were already formed as I don't think the show said when the group was formed but my guess is they were already formed during that time and were abou to kill the guys sinc they were powerless but the Darkness realised something, probabl that their powers would return so instead of killing them now, the Darkness lets them live so that when their powers are restored he is now totally regenerated.
So they got their powers back and the Darkness is regenerated. How? Most liekly bycreating a copy of the original body he had bt this time a maybe more stronger body. The Darkness finds that Blaire is not followng orders so he kills blaire with what many people assume is the Black Widow Blade because it glows red and the blade is black but listen.
The Darkness can turn any beam sword's blade black by using it, so this may be another beam sword or by further speculation,it may probably be Mario's sword since his sword glows red as well.
And that's my theory on the Darkness' return what do you think?
But you must have known that already...