Yeah I wondered that too, but I think the power of darkness is in the trees eye. Perhaps the tree being activated has shrouded the planet in darkness, and prepared the moon.
Also did Obito know about everyone being connected up to the tree? I'm guessing he didn't but Madara does, Madara's full intentions haven't really been revealed yet but I bet it's something pretty dark. It could be something really out there such as he wants to charge up that tree with people's chakra like a giant battery, and use the energy for something, such as rewinding time to confront the Sage about the Uchiha Stone Tablet,:nuts: -that seems to be written about him oddly enough in particular. It could even be that he wants a rewind to go the point of his fight with Hashirama so that he could try again lol.