One step at a time

You take this one step at a time. Once you have the captain under your control taking over the rest of the ship will be much easier. As for getting to the captain's room there are vents that run the whole ship providing everyone with fresh air and as long as you have someone to guide you and someone else to shut of the sensor so you not caught it should be easy.
Lucky for you commander Joan knows the ship so can guide you and her tec canzy can turn the sensor off for a sort period of time with getting caught.
With that you and Joan go into the vents and she leads you straight to the captain's room.