As any fan of Cthulhu knows, the old bait n' switch is a classic and useful trope to play in a game. Basically you give them Mission A to accomplish and then B happens which is far more exciting/horrific/dangerous.
It makes a difference in horror terms too. If you tell the PC's that they are going down to investigate a planet which has ceased all communication and there are no life signs, then they mentally prepare for an Aliens type of scenario and ask for Marines and tac-nukes. Using the same scenario but telling them that they are going to pick up a prisoner then they prepare for a milk run and the horror of the empty planet and questions of what happened are far more terrifying. The horror works because its more of a shock, the Players feel less prepared and the uncertainty and doubt is much greater.
So what are Standard Acolyte missions that the Inquisition can plausibly use the PC's for? Stuff that doesnt require an Inquisitor presence, and that the Acolytes should be able to handle with minimal resources and some independence?
Here are some ideas.
:Escort a nascent psyker from a small population centre to the Black Ships.
:Hunt for a minor Heretic who may have leads to other Cult members.
:Survey a cleansed planet for any remaining Xenos taint, 1 to 100 years after the Guard victory over Orks/genestealers/Hrud etc
:Administer Voight-Kampf tests in a hive or vast Adminstratum complex as a routine screen for non-human infiltrators. (""You're in the desert, you see a tortoise lying on its back, struggling, and you're not helping -- why is that?"")
: Investigate Omens and Signs on behalf of Ordo Malleus- going to remote villages to document rains of blood, 2 headed-calves etc. They might be real, they might be drunk peasants, but the Daemonhunter needs to know.
:Transport a prisoner back to the Inquisition base.
:Liase with Adeptus Mechanicus/Adminstratum/Arbites officials over some new discovery and determine if it warrants an Inquisitors personal attention
Any more?
SJE