I've decided to create a fish bowl to swim around in and get their feet wet. The fish bowl concludes with the player group escaping, and in the process the player Rogue Trader will inherit his or her charter.
The players are marooned in a system, that has been influenced by a warp flux for 500 years. Their ship has been orbiting the main hive world the entire time, the original captain has long since died and the player is the second son of the current captain. The vital elements of the crew (navigators and astropaths) have been kept in cryo. The crew has dwindled and occasionally restocked from the planet below and some of the outlying colonies or orbital platforms when needed. Indeed, by some peculairities of the flux, a few ships have arrived in-system and couldn't reenter the warp (a-lead-in for other player characters that don't want to be tied to the system).
The system itself is composed of the main hive world (which suffered greatly when the flux occured), a bombed out feral world (a previous rival of the hive world) and a scattering of mining or orbital platforms on the other celestial bodies. There is a small navy detachment, which has degraded over the centuries and mostly crewed by locals, rather than pure navy; the same can be said for most Imperium institutions within the system.
The flux has shuddered recently, which could mean the end of being trapped. The astropaths and navigators are roused from their slumber to get a feel for the situation (imperial tarot?). Ominous portents are revealed with the news the flux will indeed end soon. The players are tasked with visiting their planet-side operations and revealing the details to their planetary envoys.
The players start the game, going to a eco/political ministry meeting with their envoy, which entertainingly will end in a gun fight, which breaks out, naturally when the players envoy is speaking. The players get arrested by local authorities who blame them (innocent or otherwise), but it's quickly overturned by the Adeptus Arbites and the players get a navy escort back to their cutter - and get to meet the navy commander who brings bad news: their was an incident on their vessel of critical importance and they must return immediately.
Upon their arrival they find that danger is afoot: someone or something sabotaged all the cryo pods, the astropaths/navigators are dead.
Any psker born in the last 500 years has been executed by Witchhunters (Inquisitor?), because they could not be returned to Terra to be tested. The only way to leave the system is to track down any 500 year old astropaths in the system and get them to the vessel. The senior crew is dispersed to track down any leads; the players included.
And that's how is starts. I might include 'pseudo endevours', namely they get a 'chapter house review' about their performance, which would work similar to a normal endevour, but on a smaller scale (scaled to the finite resources of their vessel and the system).
A series of small adventures to collect information and find replacement navigators, and deal with both the local and naval groups.
The end results of the prelude are: The older sibling and father are killed, the player inherits the charter. They find the crew they need: they are frozen in deep storage in the naval base, which also happens to be the source of a chaos cult.
The hive word slowly becomes more riotous, until a full scale rebellion occurs - and only revealed to be a chaos cult near the end of the prelude.
The players flee the system with their replacement crew: they have to repel in-bound orbital shuttles filled with chaos cultists and those trying to flee the planet. The scene is punctuated when the now chaos-crewed frigate turns on the players and starts attacking (it gets attacked by two escorts still loyal, allowing the players to flee).
And the players escape to rejoin the rest of the Imperium. The planet will be deemed infected and suffer an exterminatus.
Is there any additional insight, or is this solid?