In the Star Trek: Voyager episode "The Voyager Conspiracy" it is revealed that Seven's predictions are basically a Borg equivalent of information overload. She is putting random facts together into a conspiracy.
However, there's one piece of evidence that seems to have evidence of an actual conspiracy: the tractor beam on the array.
Is it ever explained?
There's no major reason to assume that there was a tractor beam. Both the computer analysis and Tuvok's own interpretation of the sensor data indicate that she's simply jumping at sensor ghosts, seeing patterns where none exist. The "tractor beam" she sees is most likely the by-product of an energetic explosion combined with large amounts of unknown technology:
SEVEN: Is that a tractor beam?
COMPUTER: Insufficient sensor data.
...
TUVOK: Speculation is not evidence. There was no tractor beam, because there was no ship in the vicinity to generate one, unless you can prove otherwise.
In reality, such abberant pattern matching is known as apophenia, the tendency to see
" abnormal meanings in the entire surrounding experiential field"
Seven is suffering from an advanced form of this condition, made worse by her extreme knowledge of cloaking technology:
JANEWAY: You're right, Seven. There is a conspiracy here. But I believe it's a conspiracy of one. I've got a theory of my own. Your modified alcove threw your synaptic patterns into chaos and your mind can't make sense of all the information, so you're generating theory after theory in an attempt to bring order to that chaos.
