Freelancer has often been called the king of Acceptable Breaks from Reality due to little things like the fact that everything in Sirius is apparently on the same plane and is astronomically speaking a hop, skip, and a jump away from everything else. Most simply write it off as being a necessary compromise with reality in order to make the game playable. However, after reading the Nomads' backstory written up by one of the game's original creators, the possibility emerged that the outright bizarre characteristics of Sirius that we see ingame may not be (merely) the developers taking the pragmatic approach, but may in fact be the result of the Sirius Sector being largely created by the not-so-resident Sufficiently Advanced Alien gods known as the Daam K'Vosh. Needless to say, the entire game could seem quite a bit more ominous now.
Also, there's nothing stopping individual systems from being oriented differently to one another, the same way as Earth's real-life solar system, which is inclined by roughly 60 degrees relative to the galactic plane. And even though the overworld map shows all the accessible systems relatively in one plane, with spans of light-years between them, they could individually be up and/or down quite a distance away from the apparent 2-D surface.
New York City has been referred to as "the center of the universe". The game starts with Trent looking for work on Planet Manhattan, in the New York system. If you open the map and expand to the Universe View tab, New York is at the center of Liberty space, which is dead center in the Sirius Sector.
In one mission, the Liberty Battleship Unity is engaged and destroyed by Attack Group South. Not the first time a defecting South destroyed Unity.
The Gameplay and Story Segregation between jump holes supposedly being "dangerous" and actually being perfectly safe in practice makes sense when you consider it's Ageira Technologies, who make jump gates, saying this; of course they'd want people to use their products!
By the end of the campaign, it becomes pretty clear that the attack on Freeport 7 was intended to destroy the MacGuffin Artifact that is later used to remove the Nomads from the Sirius Sector. It's a Near-Villain Victory before the player can even do anything, and according to Trent's log, he had only seconds to get to an escape pod in time to save his own life.
Just how many people are possessed by the Nomads over the course of the campaign? Especially early on when the player has no idea what the cause of The Conspiracy is ...