During the first mission of my new rogue trader campaign, the dynasty is commissioned by the inquisition to search for a mission ship in an unexplored system in the Expanse. Their goal is to find a secret Yu'Vath treasure within said ship (though the exploreres only know that they are looking for a sealed cargo with an inquisitorial insignia on the side). After a long, and lets just say interesting investigation of the system, they find the ship they're looking for floating in an asteroid field with many tears in the hull and only a faint glow of life radiating from the bridge. There is a faint distress signal that is being interfered by the asteroid field and the sheer damage to the ships systems. When entering the ship the party split into 3 groups each with a unit of 10 armsmen escorts, one searching the bridge, one searching the cargo hold, and one searching the engine room. The party finds a gruesome scene all over the ship that would make Khorne dance with joy. The crew has been brutally murdered and various bulkheads and hallways of the ship have collapsed leading to dead-ends. After a brief exploration, each party is attacked out of the dark as a Rak'Gol trap is sprung. Basically they are initially hit by overwhelming odds that the party members must run and the armsmen are destroyed in CC. The first part of that session had to be cut short and now i'm wondering what to do now. I plan on the RT ship being attacked by a Rak'Gol, but trying to figure out what happens along the way with the party to reorganize and get back to the ship, while at the same time giving it a survival horror feel. What should I do?

In my campaign, I had a situation that was quite related to what you described. The team that entered the ship was attacked by lurking xenos (something like Tyranids) while the Rogue Traders ship got threatened by further ships.

The team inside the stranded ship had to repair its weapon systems so they could fire out of the wrecked ship onto the enemies to support the Rogue Trader ship's firepower.

This twist worked very well and gave the whole situation a survival-atmosphere: The team inside the wreck had to get access to special areas of that ship and to repair them in time – while they were under attack themselves! At the same time, the Rogue Trader in his ship had to coordinate the defense of both ships. The time-pressure was the ingredient that made the whole brew interesting.

Make them do a bunch of awareness tests, and occasionally make stuff appear basically right above/behind them.

try this: the PCs being chased by foul xenos, but they cant leave empty handed (the inquisition doesnt like failure). have them run to the bridge (which is, for some reason, mostly untouched) and seal themselves in until they can figure something out. Make them search the ship's logs for where the Cargo may be stored, and then have them stumble across a recent file, created by one of the ship's crewmen, that details- more or less- what led to the ship's current plight. create a side adventure from that, where the crewman begs for whoever has accessed the file to detonate the ship's plasma core, ending the lives of all xenos (and possibly the explorers!) aboard the ship. he offers the coordinates for a treasure planet, which can be accessed from the terminals in the engine room, in exchange for the deed. could lead to an interesting new adventure arc, what with the possibility of a planet's bounty.

Hmmmmm I actually like that option. Thank you very much for all the input. I believe I have the begin of a very interesting adventure.