I'll take a crack at this! I enjoy doing word puzzles and teasers.
Watcher and Sim Conspire; (My guess would be William and Ava, since William pretty much has the power of a Watcher, or he at least thinks it.)
Resulting in two things nonexistent prior; (This would be the twins, Pallas and Apophis.)
One's failure to control a desire; (One of the twins strikes up a romance with Susie.)
Creates potential for raging fire. (Nothing good comes from it, so maybe an unplanned child?)
Anything dared; (Bad things happen.)
Yet only some are scared; (So it's been planned. Some are ready for the bad things.)
For the conspirators are prepared; (Someone planned for this and are ready for action, maybe?)
In their own web they shall not be ensnared. (No matter who planned it, they're not going to be caught.)
One is unused to being played; (William or Ava, I suspect.)
For its own web was laid; (IT'S A TRAP!)
But now suffers the masquerade; (Now the costume party's over and everyone's been unmasked. But did William lose the contest?)
Whereas previously, another had been betrayed. (Do unto others as you would do to yourself would be the moral of this story.)
And that's my guess! It's probably wrong, but it was fun to think about it!
Also, having Susie be the red shirt makes since. But who would be Spock/Kirk?