I'm getting ready to run a pair of 40k stories, and I am pretty sure there are published versions of these ideas (there is nothing too original about what I am looking to do).

What I was thinking of doing was run two short games. First, start with DH or RT. Have the team go on a mission to recover and artifact of some sort. They will collect it and end up on a ship taking it home. Or perhaps, they’ll put the artifact on the ship, go their separate ways, and then find out the ship with cargo was lost.

Next game will be Deathwatch. On a routine cruise on their way to crush a Chaos insurgency, they will come across a space hulk. Standing orders are to check them out, least of all to purge any xenos that might be on board. During the course of checking the hulk, they’ll (at least the players) will learn it is the ship with the artifact their group initially liberated.

I thought it could be a cool twist. Perhaps might play with time travel a bit. I was originally thinking the Death Watch team would be 500 years after the RT group, but then I thought, what if the ship traveled back in time, and the DW marines had to make sure the ship was found by the RTs in the future.

At any rate, I haven’t cooked up the details. Do you know if there are any premade adventures like this out there? I’m sure I’d be better off running or modding a premade than trying to put it all together from scratch.
 

There are, actually… MINOR SPOILERS BELOW!

If you wanted to run the Lure of the Expanse adventure for the Rogue Trader group, but replace the rewards for that adventure with your xenos macguffin, you can have some fun. It's a pretty solid adventure, with a couple of nice twists and turns… jsut be prepared to think on the run, cause the pre-written plot seems to entirely forget that players have free will and a malicious delight in destroying stories (my theory, anyway).

Then for the Deathwatch team, if you run the adventure in the core book and follow up with Obluivion's Edge there's a section where your players are travelling through a Hive Ship where they come across a partially digested Imperial Escort…

For the space hulk / ancient ship you might also try out Broken Chains (an introductory adventure for Black Crusade) or Shades of Twilight (second adventure in "Purge The Unclean" book for DH).

Great. Thank you for the suggestions. I will take a look at these and see what might work.