Okay guys. Basically, I've recently managed to set up a RT group, and my friend is GMing this. He's clearly a lot more comfortable GMing than I am, but he barely know the rules. So, to help us both, what I've suggested is that every now and again we swap positions, where I GM while he plays for a bit. So, I've started planning a short Endeavour for the group to participate in, that will hopefully act as a side-quest to not distract too much from his main plot, while also adding in a potential recurring antagonist/ally that he can use or not. So basically, here's my plan for you guys to look over:

It starts out the usual way, with the party entering a tavern and inquiring about work in the local area. The barman nods to a man sitting with his back to them, and explains that he's looking for a crew with a fast ship and keen minds, if they're up for it. Upon approaching this man, they notice that he appears to be wearing a uniform, though not one that they recognise. He introduces himself as an Arbites Intelligence Officer, and begins to describe the job.

He narrates how a few weeks ago, he was approached by a man. This man related to him a tale of a criminal organisation named Orion, who have men in the repair sections of the orbiting spacedock sabotaging the warp drives of the ships they repair, and also have a small fleet of raider ships that can swoop in and steal the now-crippled ship after its engines cut out mid-voyage. The arbites officer asks the party to attempt to infiltrate this group, and either gain a position of trust or briefly sabotage their operations, whichever seems easiest. He then explains that repair dock 3Beta seems to be the one they work from mostly, so perhaps visiting that might be a good idea.

Now hopefully, at this stage the PCs will visit dock 3b with what is obviously a raider-class vessel and inquire about any work in the area. If not I'll try to improvise something that gets them roughly on the correct path. After some interaction with the various members of Orion, they finally meet someone with authority, who explains that as a test he'll allow them to go after a transport they recently sabotaged. However, to make sure of their loyalty, another ship will be sent along with them. They are told to visit a certain bar nearby at 7pm each night, and order an amasec, Zayth-style (I'll mention this to the players as an opportunity to go shopping and stock up). Once the transport sends out its distress signal, an Orion operative will come to get them ready, and that drink is his way of recognising them.

Upon meeting the PCs, this operative will explain that he is the man who initially went to the Arbites officer with information, and that they can trust him, fully.

Upon reaching the transport (assuming that the navigation rolls resulted in them making decent time), they arrive to discover that the other raider hasn't yet arrived. The transport then hails them, assuming that the party have come to help them, and claiming that they can pay well should the party save them. At that stage, the Orion raider arrives, and invites the party to launch the first salvo. I'll leave it up to them whom they target.

Upon returning to wherever they set out from, they will get a minor reward in PF from either Orion or the arbites man, along with a promise of future work from their chosen side.

So, what do you think? It's probably worth mentioning that the party arch-militant has Enemy (Arbites) and Peer (Underworld), so I can predict which way he'll swing fairly easily.

I'm sorry, I hope this doesn't sound harsh. Now you're scenario is actually pretty good, but needs some tweaking. Again, not trying to be mean here...

Your Rogue Traders (with a ship that can destroy worlds, the wealth to buy systems, commanding tens of thousands of men) go into a tavern...and inquire about work?!?!

And someone with the wealth necessary to employ an ancient warship and 30k+ crew is just sitting in there waiting to hire them?

It feels like a CEO just walked into a bar in Omaha and inquired about defense contracts and there happened to be a 4 star general sitting there waiting for a just such a CEO to walk in who owns their own personal star destroyer.

Ok, so the 4 star general is going to "test" the CEO for loyalty (the CEO also being a Duke with immense power, respect, and contacts, and a family history of service stretching back 1000 years, he is obviously unknown and untested and must be run through a rigorous interview process). The CEO and his board of directors must sit in a bar until they recieve a distress signal, at which point someone will come get them and they will immediately depart on their star destroyer (these ships being known for how quickly they can depart from dock). Now they are going to spend several days getting to the edge of the system, enter warp, and travel for a few days (I figure this must be the case since you are involving the Navigator, as you don't use the warp to travel in-system, and you don't need Navigators for "short" jumps of only a few hundred lightyears).

Now the transport hails them and tells them they can pay well for their help (presumably in lucrative trade routes or lost archeo-tech which they can trade to the ad-mech for favors, since actual cash transactions are so far below a Rogue Traders notice as to be explicitly omitted from the rules, with accompanying notes as to why a Rogue Trader would never bother with such trivial things, and why it wouldn't even register as a profit factor increase).

Next they will be given the opportunity to choose a side (good GMing there, not railroading, providing interesting and meaningful decisions with future consequences and allowing them to choose the path of the campaign. I like it).

Are you seeing the disconnect here? You're trying to run Rogue Trader (a game where some of the most powerful individuals in the galaxy vie with eachother for the control of entire sectors of space, with fleets and armies at their disposal) like a D&D game (a game where five random moderately skilled people stop in taverns looking for work, and occasionally delve into old cavern systems, kill what lives there, and take their stuff).

So, suggestions:

You're scenario is actually pretty good, it just needs some "scale" tweaking.

Instead of inquiring in a bar the senchal could be approached when they come into dock (people looking to hire Rogue Traders don't wait in bars, they seek them out. The PCs are important people with important stuff to do, they don't "tavern dive", and when people want to hire them, they go find them).

They pilot a Star Destroyer, not the Millenium Falcon. Docking and undocking is a big deal, like when an aircraft carrier leaves dock.

It can take days to reach the edge of a system and enter the warp. 40k is not a "fast response" type of universe like Star Trek, it is more like the "age of sail" where trips take days, weeks, and months. They could be instructed to wait in the warp at a certain location and wait for a signal.

In order to make it a meaningful decision (and meaningful operation) the ship needs to have something on it that might actually represent a Profit Factor increase. A high ranking member of the Adeptus Custodes or Ecclesiarchy, a piece of lost Archeo-tech or Xeno-tech they can trade. Profit factor increases represent long term business investments or increases in influence, not someone paying them thrones. Even one million thrones would not register as a PF increase.

Rogue Trader is a very different game than most RPGs, and can be very difficult to GM for people who aren't prepared. Most games focus on a "party" of 4-10 people, and their personal wealth and power. They fight evil guys, take their stuff, and do it again, possibly saving a kingdom in the process.

Rogue Trader focuses on the leaders of a dynasty and its growth. The players start out immensely powerful and well respected, kings among men. They rule a kingdom, their ship is their castle. Fleets, empires, and rival rogue traders make up your antagonists. Worlds and star systems make up your rewards.

It is a different kind of game, but if you can get the vision of it you will have a lot more fun than if you try to shoe-horn it into a D&D mold. And eventually your players are going to realize that instead of fighting your monster in a can, or your big bad, they can just send in a few thousand troops or destroy the continent from space. If you haven't adjusted to the scale by then you are to have two options: 1) the players ruin your scenario 2) you have to be a bad GM and make up dumb reasons why they can't do what they obviously can do.

The 'inquiring in a tavern' bit can still be serviceable, but will need some tweaking : the 'tavern' would have to be the planet's most upscale and expensive ressort. Something akin to the Burj al Arab in Dubaï (a 320m tall hotel with 202 suites only. the smallest being 170 m²), though by Rogue Trader standards the real world Burj al Arab would be barely acceptable for a civilized plant...

Basically, if the place isn't expensive by the local Bill Gates or Warren Buffet's standards, it's a dive from a Rogue Trader's point of view... Unless he need some underworld connexion, a rogue trader would arther shoot himeslf in the foot rather than stepping in.

A more rogue traderish setting for such an encounter would a reception organized by the planetary governor - such social event are frequently the occasion for all kinds of discrete meetings between peoples from the upper spheres of power. Of which a Rogue Trader is a member, even if he's near the bottom of the pile amongst his peers.

Right, both useful comments. I'll probably change it so that the traders are in fact approached as they enter the dock. I'll have them approached by Orion straight away, and have the person who joins the crew (with the given reason being that he knows the rough location that the transport will break down, and thus can direct them to the waiting point) fill them in on the Arbites officer and the other potential route they can take.