So I've been playing Warhammer Space Marine for xbox 360, and decided I wanted to try to base a Rogue Trader Campaign off it, mixing in the warpstorm trilogy for length and flavor. Now I only have the first two installments so far, but it seems I can work them together fairly easy, yet I'm still having trouble intertwining the two. Anyone have some ideas for a fellow GM?

For those who havent played, Spoiler Alert:

Space marine follows a squad of marines on a Forge world invaded by orks, in order to protect a Titan manufactorum from the greenskins. Somewhere in the fray, they discover an inquisitor is also planetside, who sent a distress signal to find help to protect an experimental weapon that if fallen into the wrong hands could "make him unstoppable". They find said inquisitor, help him retrieve the power source, some capsulized pure warp energy, then proceed to power the weapon by aiming it at an orbital spire. once the spire is struck, a warp portal opens up and its revealed the inquisitor has been a dead puppet of a chaos marine who is now looking to use the power to daemonize himself and become immortal.

Now for current games setting so far:

The current lvl 1 RT's father has recently and mysteriously disappeared in the unbeholden reaches along with the dynasty's flagship, thus new guy inherits the warrant, without a ship. Along comes an inquisitor who states the ship is of a large concern to the mechanicus for its archaeotech design, and to the ordo xeno's for a relic that was discovered before the disappearance. the inquisitor hands the explorers a Thulian Explorator vessel to use to find their lost flagship, and crews the ship with plenty of tech priest's and hidden acolytes (including the false man seneschal) to moniter their progress. First stop is Damaris, a known trading hub where Rogue Traders can be found to inquire about the region, rumours, etc, when an invasion starts. pretty solid start, but once frozen reaches nears an end, I'll need some new plot hooks

I've recently picked up LotE which seems to mesh a bit easier so far. still having trouble with all the minor details stringing things together, but I'm thinking having the seven witches lead towards the lost ship/relic onboard, or even to the planet the chaos dude from citadel of skulls is on. (I've only so far just skimmed CoS, only heard bad reviews but might try anyway)

I suppose my biggest problem is debating weather finding the ship should be a long term grand endeavor or a short common endeavor, just to get them their ship so they can focus on other things.

Depending on storyline so far: You could have the what the plot-inquisitor said about the ship being important to the mechs and ordos xenos a lie because really it was requisitioned by the chaos-puppet-inquisitor who became the false puppet of the chaos marine(hence is now chaos marine flagship, also chaos marine killed father now players have a reason to want to kill him). Not that plot-inquisitor knows that, he just knows that Puppet-inquisitor disappeared and plot-inquisitor is the only one that knows that Puppet-inquisitor requisitioned father's ship.

And that by imperial law the inquisition would have to pay some restitution if it was known the ship was destroyed in a mission sanctioned by the inquisition. Not enough to buy a new ship but enough to be annoying. Such a thing might get in the way of Plot-inquisitor's next promotion!

Such a thing might change the senechals loyalties (who wasn't let in on it).

Give them a glimpse of father's ship when they're going through the warp in the middle of a growing warpstorm. Make it annoying to get to. When they get there hit them with orks. Maybe make them outnumbered but then a space marine vessel shows up and helps them. Maybe they get boarded and then space marines come out the ork ship to kill the orks invading the player's ship. (having cleared the entire Rok)

Alternatively you could have them attacked by a pilgrim ship full of cultists

led by this guy

Rogue missionary name: Kennoch Roth
WS:35 BS:21 Str:40 T:41 Ag:29 Int:32 Per:33 Wp:49 Fel:42
Awareness
Charm
Common Lore(Abominated Imperial Creed)
Dodge(Ag)
Intimidate(s)
Forbidden Lore(int,Nurgle+10)
Search(Per)
Wounds: Base 15 +? From nurgle.
Initial rolls:3

Daemonic, Fear (2),
and From Beyond Traits.
Ravaged Body:3
Nightsider: The mutant gains keen eyesight, allowing it to see clearly in areas of low lighting. It gains the Dark Sight
Trait, but takes a –10 penalty to all tests when in the area of bright light, unless its eyes are shielded and skin covered.
Fear 2: Frightening –10, Willpower test. Page 294 if it fails.
From Beyond: Immune to Fear, Pinning, Insanity Points, and mind-affecting powers.
Daemonic
Daemonic creatures are creatures of the Warp, but can
manifest in realspace either through sheer strength of will,
hunger, or occult rituals. Creatures with this Trait double
their Toughness Bonus against all damage, except for damage
inflicted by force weapons, psychic powers, holy attacks, or
other creatures with this Trait. Daemonic creatures are also
immune to poison and disease.

Dark Sight
A creature with this Trait sees normally even in areas of total
darkness, and never takes a penalty for fighting in areas of
dim or no lighting.
Misshapen: The mutant’s spine and limbs are horribly twisted. The mutant may no longer run. (-6 agil calculated)

Malformed Hands: The mutant’s hands fuse into slab-like appendages. Reduce its Weapon Skill and Ballistic Skill by 10(done)
Furthermore, the mutant takes a –20 penalty to any test requiring fine physical manipulation.
Grotesque: The mutant is either badly deformed, scarred, or bestial, marking them as accursed and impure. The mutant
takes a –20 penalty on Fellowship Tests made to interact with ‘normals’, but gains a +10 bonus to Intimidate Tests.
Weapon:
Chainsword: 1d10+6, pen 2, balanced, tearing
Flamer: range20m, ROF S/-/- Clip:6 Reload:2 Special rules Flame (use template)
Guard Flak Armor
Perverted book of saint Drusus: +10 to abominated Imperial creed.

I rolled 3 times on the mutant table and rolled 100 on the first roll, and then 3 more mutations on the second. Deamonspawn ended up being the only significantly good roll though.