Great Old Ones are considered to ‘control’ Nodes when their tokens occupy that location at the end of the Combat Phase, prior to the Conjunction Ritual phase or before play passes to the next Great Old One.
For most Great Old Ones this will mean that they must have at least one Cultist token in a Node for it to be considered occupied and under their control. In the case of Nyarlathotep, their Servitor Race, the Serpent People, has the special ability to occupy Nodes along with their Cultists.
This means that unoccupied Nodes are considered ‘uncontrolled’ Nodes. If a Node is ever abandoned during any phase of a Great Old One’s turn, it immediately reverts to being ‘uncontrolled’ and whatever active effect of the Node Deck ceases with the Node Counter turned with the description face-down and the corresponding Node card returned to the deck until the Node is occupied again.