and scores a 'hulked' on the critical hit chart. (BS roll with 4 degrees of success, rolls a 10, 10, 9, 4 and +8 for the sunsear laser battery).

Then the Rogue Trader Captain uses his 'Intimidate' to order the second pirate ship to stand down - and rolls a '1': 5 Degrees of success

I'm running the group through the treasure ship adventure at the back of the RT Core rulebook. Funny enough, they never actually talk about what to do if/when your RT crew manage to capture a prize ship intact. How have other GM's run it? Because I guarantee, my RT Crew want to keep the ship.

The encounter itself is the one where the Pilgrim's Traveller is found drifting in the Battlefield, en route through the Maw. One consideration I had was to space the Raider's command crew (keep the indentured crew who had no idea what was going on), take the pilgrims and surviving crew from the Traveller, put them aboard the raider with a delegated command staff from the PC's ship, and strip the Traveller for parts. Make it out of the Maw intact, and work things out upon arrival at Footfall?

Taking ships as a prize after a battle is one of the most common ways in RT to adquire your ship, so if you are a GM get used to it because it's going to happen fairly often. That's why Boarding actions, while risky, are an excelent way to get a new ship without chances of destroying it.

New ships can be used in several ways:

1) As combat support for the players ship. That means your players travel with one or more NPC ships they have.

2) As ways to complete certain Endeavours. For example, if you capture a Transport and you start a new Endeavour which focus on exporting some goods for a planet in the Koronus and selling it in the Calixis, you can perfectly use that transport to permanently deal with that (the players loose the transport, but they completed one Objetivo toward an Endeavour of makign a permanent trade line of certain goods).

3) They can travel independently of the players to perform several Background Endeavours (look for the rules inside Into the Storm). While risky, it's a good way to increase the group's Profit with less interesting Endeavours while they focus on the cool ones.

I answered this question on another post somewhere, and here is my thoughts on "acquiring" another ship.

The "acquired" vessel might be owned by another Rogue Trader House, or an Imperial organization, or even by the Imperial authorities because they deem it too tainted to be salvaged. Say a Raider ship was lost over 4 decades ago, they (another House) wrote it as destroyed, and cheated the Navy/Administratum/Mechanicus out of Insurance/Compensation Thrones because they (the House) claim the ship was doing a specific hired job for that Imperial organization. This means it is now legally the new RT's ship once they file the proper proceedings. On the other hand, an "acquired" Transport ship was written as captured by pirates a decade ago, and the owners have a reward for anyone that recovers said ship, and still want it back.

Of course, the PC's could strip the Transport ship, and give it back. Or the Dynasty no longer has the funds/doesn't exist any more, and is now the PC's ship. It may come to pass that the PC's never report either ship to the Navy and/or Administratum as belonging to the players House. This of course has the effect that the the Navy (and Rogue Trader's with Navy affiliation) will investigate the aforementioned ships once they come across them in space/a docking station/etc. Kind of like they scan the ship as it gets close to port, discover that its listed as a chaos ship, and shoot first and ask questions later. Your new ship, is now toast.

For some reason I thought they clarified some of these issues in one of the new supplement books, but since I don't have any of my books with me, I'm probably wrong.

And yes, just as Maese Mateo said, it is the most common way players can acquire new ships. But this will also require new crew, repairing the ship, and possible getting the ship to those locations (all this could take months or even years game time). Getting an incompetent crew should be easy but still costly, but getting Navigator or Mechanicus personnel will probably require some endeavors to get them to say yes, not to mention a lot of funds unless the endeavor was of epic proportions.