Destination: Unknown
The drones detect smaller areas of the pyramid ship that have similar magnetic fields. Most are small, but one is man-sized. The smaller ones are probably weapons ports or access hatches, maybe a mix of both; it's hard to say. The drones' magnetic pulse only opens the man-sized one, so that's probably an airlock.
Since the Scout ship had its reactor completely powered down... i.e. inactive and inert... it'll take about an hour to power it back up. That's a safety precaution. It can be scrambled on in about 5 minutes.
However, Serge can lift off from the pyramid ship's docking bay using his auxiliary batteries. He's only got about 6 hours of engine thrust off of the batteries, though.
Also, remember, there's a much larger ship parked directly overhead of the docking bay. There's not enough clearance for him to get clear of the pyramid ship unless the Long Shot moves.
Sam can easily display any of the ship's systems on her console, either halved, quartered or tabbed. Unless someone locks out that particular system from the command or primary console, she has just as much control over it as the other operator.
She still can't get any readings on weaponry, neither through the docking bay nor the airlock when the drones get it open.
It seems reasonable that the pyramid ship's flat square side is probably the base, but that's assuming the builders constructed it either on a planetary surface or with the intent of landing. However, if they were really alien and built the ship in space, the 'base' could actually be the leading edge.
There is no indication yet of which is the case.