The black cloud was the black gardens heart. Not the darkness.
Think about it like this. Guardians=light. Everything else is simply -blam!-ing darkness. That's it. Everything is. It's alllllllllllllllllll the darkness.
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Are you getting mad? Lol I know year one destiny didn't have much story but it did have some. In the opening video you see this black looking cloud callee the darkness chasing the traveler. Then later on in the story mission you are tasked with going into the black garden, and slaying the darkness at its heart. Play the mission again and clean your ears out. If you want to start getting all ornery then you can, it's not going to change anything about it. And guardians are not the light, they are forged in light but they are not the light. I know the metaphorical story that is destiny is really hard for people to follow because there is so much abstract concepts but the light and the dark, but it is only a symbolizing the fight between what helped us and what hunts the helper. It also doesn't help that be creature is white and the other is black. But in short, that is a creature, and you kill it. And, surprise surprise, it has the ability to resurrect (three big ass vex) just like the traveler resurrected you through its fiduciaries, the ghosts.