You choose the option of asserting your ability to pilot the airship over that of all the others on board.
** cutscene **
You sit in the pilot's seat, as you suspect that the command interface may take a while in its data processing. However, an error message pops up on the screen, insisting that you are not, in fact, the most qualified person aboard the airship to pilot it. You close out the message, and look up how to conduct searches for people aboard the ship, receiving a detailed video on how to search for passengers and crew by name and by rank. After watching it, you open the Surveillance section and conduct your search. First, you look for the most qualified person -- the Captain. You get the response: "Captain is aboard the vessel. Captain is deceased. Captain is no longer capable of piloting the airship."
Next, you search for the Lieutenant, and receive a similar, but much stranger message: "Lieutenant is aboard the vessel. Lieutenant is deceased. Lieutenant is capable of piloting the airship." You refresh the page, but you get the same result. "Lieutenant is aboard the vessel. Lieutenant is deceased. Lieutenant is capable of piloting the airship." You check the location reported for the Lieutenant on the screen, and see that the deceased Lieutenant is the kitchens, just beyond the first class dining compartment to the left. You decide that he must have died there when the skeletons arrived.
Since the computer is reporting that the Lieutenant is able to fly the airship, you start to head in the direction of the kitchens, just to be sure; any pilot with real flying experience would be better than a kid whose only flying experience comes from online flight simulators of jet fighter airplanes. Just because the result is so odd, you decide to refresh the page once more to see if the command interface made a mistake. However, when you refresh it, you see that the location of the Lieutenant is now the first class dining compartment. You hear a mighty crash and splintering of bone behind you in the next room, and you turn around in the chair to see what the noise is. You get up out of the chair, and peep around the edge of the doorway. Looking around, you see that the two tables at which the skeletons were sitting are overturned, and the skeletons are in pieces. You see no sign of the reportedly deceased Lieutenant. Addled, but somewhat relieved, you turn around back into the cockpit and see right in front of you a large creature, ten feet tall, with four long, spindly legs of ivory white. They all draw together in the middle at a quite normally-sized torso which is covered with an Royal Air Force uniform; when your gaze is done there, your eyes finally reach the head, with a disproportionate and discolored face on it. This fearsome creature stares at you for a moment, and then walks over to the chair in the middle of the cockpit and sits down in it. Two of its legs press buttons and pull levels, while with its hands the creature pulls on the joystick, righting the airship from its earlier tilt. Then, it sighs, and it starts to cry silently.
This, you surmise, is the Lieutenant.
** end cutscene **
(I'll probably put in cutscenes every once in a while when the player reaches a crucial plot point and I don't want them to have to figure out just the right way to do things through trial and error and un-subtle hints by me.
(@Steelfist: Nope, and nope. I'm just making all of this up as I go. I had no idea that there were kitchens beyond the dining compartment, or a Lieutenant who is warped in ways you'll only find out later, until I posted it just now. I mean, I kind of had the idea that there needed to be an NPC, and that he needed to be a badass non-human ('scuse the language, sorry), but that was all rather nebulous in my head.
(Oh, and in case anyone was wondering, I'm modeling the combat system somewhat off of that of Dark Souls and partially Skyrim, in that there's no such thing as a "turn", and you can win a fight no matter what you've got on or are wielding as long as you're willing to micromanage combat enough to the point where you don't get hit. In that sense, basically there's no limitation on what you can fight or do at any given time -- it's just going to be harder or less hard, depending on the quality of your equipment)