I want to run a scenario past you all, as I'm really fond of the Warpstorm Trilogy, minus some of the middle bit. Fear not, though; I'll endeavor to NOT spoiler the campaign, beyond two names you'd know almost from its beginning. I'm going to use my current project, because it gives me context, and because I like to blabber about my works (viva shameless self-promotion!!!) So stuff with Qel-Drake, the Tau, and yada, that's mine, not WST.

So, the WST hs wrapped up, and Qel-Drake and Co. (you) won the day. You are sitting there, licking your wounds, and counting your thrones. A little time goes by and you learn something terrible; a small coalition of Tau have begun to sneak into the Expanse, assisted by renegade Eldar, giving them supervised access to the Webway. You might not know all of that, since its some Eldar you know who are telling you, but you decide to go tell the battlefleet about this threat. Good news, they decide to take action, but the bad news, you found the Tau, and they expect you to assist in dealing with them. The Exalted Wyrm is a kitted cruiser, so at least you're somewhat qualified. Now, here's the scenario:

Captain Locke has been through a lot, lately. Disobeying orders repeatedly, battling Orks, some Chaos, saving several worlds, and maybe the entire Expanse, but her superiors are still irritated with her, for her insubordination. Deciding to punish her, they call her to station. She was going to be court-marshalled, but one Admiral, at least, is an ally, and he flexes some muscle, as it were, to get a different ending. Locke is "allocated" to Qel-Drake, for the term of ten years, or until the Tau threat is neutralized, whichever occurs first. They were going to mothball the Aegis , as it's old, beat up (they sold her sister ship decades before, maybe longer, so they can do this), and its captain is being tossed, but Qel-Drake throws some money at the problem. The Navy isn't interested in selling him their ship, even to help, as he's not fantsticly in with them, like his dad was, but Qel-Drake negotiates, saying he'll pay the ship's upkeep, and Locke will maintain command of it, under Qel-Drake's orders (they know she'll resist if he gives questionable orders). A third warship to help fight the Tau will help greatly. When the term is up, she, and the Aegis , will go back to the Navy. The Admiralty see it as a way to use Locke as she seems to behave, and also possibly embarrass her back into good behavior, as Qel-Drake could blow it, and having to put up with him for 10 years might be more than any sane person can handle. Admiral Kossal takes her aside, and tells her not to see it as all bad, though. The Tau are evil, nefarious, and subversive. Locke is all about saving the lives of the people, and there are many such people she could save doing this. If they fail, many worlds may have to burn for being touched by the Greater Good.

So, could a Rogue Trader get an unpopular officer, and their ship, temporarily assigned to his service, with a handful of caveats, and his own footing the bill, or would they just say "to hell with that?" I sort of like the idea of Locke, when all is said and done, maybe even earning a Warrant of Trade, for another job well done, that she might continue to help, in her own style, without hampering the Navy, and that ship is already hers in so many ways. She'd also be a good ally, and have a good ally in two other Rogue Traders (Aedan Qel-Drake and Isabella Artymus), and possibly an Inquisitor (Ursula Von Cossrath), though she's a bit, umm, well she can be a problem, but what radical OX Inquisitor isn't? I sort of like it as a continuance for the character, once Warpstorm Trilogy is concluded, your points and plans may obviously vary, but I don't know how easily it COULD happen.

Thoughts?

In my current campaign, Article 15 of Ye Olde Warrante of Trade states very clearly that

XV. The House can, with prior notification, obtain the aid of the Imperial Navy, given the House pay for the maintenance, salaries, and battle damage of those ships. No more than ships of a suitable class and equal in number to those provided by the House shall be assigned.

Of course, my Warrante has a much more flowery script that won't transfer over to this forum.

Personally, if the Rogue Trader has an Admiral on their side (or, at least, inclined to their side), is willing to pay for the ship's upkeep, and is going to make the ship disappear into the Expanse for a decade when they were just going to scrap it anyways... yeah, that sound's like a perfect deal. The way the Admiralty would see it, chances are that Locke won't come back from the campaign, or someone else would be in charge to deal with the problem.

I would expect that they would put several provisos in the contract (obviously), place a few spies on board (that the RT and Locke don't know about), and possibly force the Dynasty to provide a Navigator; but at that point you're just haggling about the details.