I am working away on my next mission (which appears to be sucking away all my free time lol).
Anyhoo without giving too much away a group of Aliens placed an infiltration squad on your vessel during your previous encounter.I have a sufficiently nerdy explanation as to how they beamed through your shields.
What I can figure out is where?
What would be a good place for them to hide that would get little if no foot traffic during the routine course of a voyage? I dont want to set it somewhere that would seem stupid because it was visited so much by the crew that it would be implausible.
However if this idea is stretching the bounds too much then how about a tracking type device being beamed through the shields? and again where would be plausible in terms of defeating internal security sensors?
My advice would be first off, from a practical sense, look at the maps available for you to use and decide from there if you are actually having the characters search the ship for it. You may see something in one of the maps that you find interesting or inspires you. But if you were planning on making your own map anyways doesn't really help.
Personally though, I've always been a fan of in plain sight myself. Where everyone looks but no one notices. Like suddenly someone see's there is a strange new light fixture on the ceiling of cargo bay to or you never remembered that potted plant being in ten-forward before.