[@DeepestApology] Good question! Also, points for making a Mass Effect reference.

The Pilot is the helmsman, as well as the commander of the expedition while they are on the ship. So they're in charge, until the group steps foot on solid ground at the Willman Lab. They are the direct superior to all of the ship's crew, and indirectly in charge of those tagging along on the expedition because they're riding in his/her ship. So really, the Pilot will be a combination of Jeff and Shepard's roles. Except as soon as they step foot off the ship, he doesn't really have any direct authority over any soldiers or scientists who were on board.

The captain of the expedition is the Sergeant tasked with bringing his fireteam to the Willman to investigate. Essentially, once the group sets foot at the Willman, the Sergeant takes over authority from the Pilot (at least for everyone who isn't the ship's crew).