Actually it sounds like a very good idea, and I'm sure within the context of a storyline you could do it.
You can set the special ship goal as being to observe the ship, and you can use the NCB to change the type of ship you are in once the special ship goal is completed. If it's just some kind of weird cloaking device, you'll need to make a collection of ships with the same specs but with varying appearances, and you'll need to have the mission only start if the player is flying the right kind of ship.
Obviously this method will only work in the context of a mission, and you'll need to corral the player a bit, but it would (will) be an awesome effect, especially if you prepare the player by saying 'We've worked out this new cloaking device, but no-one is sure if it will work. We need you to fly to system xxx. If all's well it will adapt itself to the ships there. You can then go on to system yyy, and it should adapt itself to the ships there as well.'
If you give the system almost complete murk, then it will be a few moments before the player realises it's changed, which will heighten the effect.
It would then be nice to have some text come up when you complete the special ship goal, saying something like 'As you enter the system a weird light flashes that you have never seen before. You can't see what it is that's happened, and then you happen to look outside the porthole'.
If you want to really hammer this one, you could have a couple of missions preceding it where they try prototypes which do nothing more than change the ship's colour, leaving the player to be chased out of the system by the offended government.
Any way, good luck with this. It sounds like you have some really creative ideas.
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