I for one have asked them to roll their sanity at character creation, and use the previous notoriety of the Ventura Fortuna to be maybe haunted paired with a healty dose of the NPC gaslighting them to make the players think its actually maybe a horror game and their characters might be losing it.A question for the GM's running Singularity right now:
Have your players already discovered the secrets of the Fortuna Ventura, and how long did it take?
We're currently on our first tour along the Confederacy route, having just stopped at Bogustin. I've rolled mysterious event 8 for that week - android crew member caught in reset mode - so I made up a short event: Hash Deacon, the (android) engineer was hit by a random energy spike while in engineering, forcing a reset and having him staring into nothingness for two minutes. Of course, the PC engineer did immediately call the PC doctor and together, they got Deacon to sickbay and into the autodoc. At this point, I decided that the autodoc was manipulated, showing human lifesigns instead of an android. Still, for a single moment, the doctor saw... something non-human, before the manipulation kicked in!
Now that my players interests are piqued, they'll start investigating like a pack of hunting dogs on the scent. I could have handled the scene in sickbay differently, but the doctor's player is a rather quiet person and I just wanted to give her a scene in the spotlight.
I plan to make them suspicious on the first route and make them discover everything in the first half of the second trip. To make them allies to Naliir, I think its best they interact directly with him sooner rather than later, especially since so much of the intrigue would happen behind the veil without their knowing if they don't talk to Naliir or don't use the small ship whose name escape me at the moment. Also I want to make them do side missions.
In your case, I might make it seem like the problem was with the doctor or the autodoc if I wanted to make the mystery last longer. Or, while they are full on bloodhound chase mode, I might place the drug enduced bad trip right there to make their suspicions blow out of proportion and see what come up once things calm down.
Your energy spike in engeneering was an inspired idea, and your players worry for Deacon's health, making it that more shocking when the final reveal will happen.