Thanks for the interest! Sadly, the state of the submission is that the game can be confusing, with unintuitive UI, and some mechanics can seem bizarre.
The main game loop centers on reaching the mission, “hacking” 3 “system” nodes, and then proceeding to another ship. Doing anything other than “waiting” will raise alert levels on the ship, which will trigger more enemies to spawn and potentially trigger a ship-wide detonation. The final ship was piloted by your father some time ago, and towing it is the final mission.
To combat ever-increasing alert levels, you can close doors so that enemies won’t see you, undock and dock again (this will generally decrease high alert levels to somewhere in the middle), and generally try not to trash the place as you go.