A lot of the world of StarSector is pretty static, but I was playing Master of Orion 2 today and started thinking about global changes. Things that would temporarily warp the world of hyperspace, making things a bit more chaotic. Each would be rare, but serious. The goal would be to make hyperspace travel a little more dynamic. Here's a few interesting options:
1) Hyperspace gale: shifts around the existing hyperspace storms and deep hyperspace areas, permanently, over the course of a few days. Hyperspace travel during this period is difficult as it all counts as deep or storm, but when it passes new lanes have been opened up and others have closed. Essentially, this recreates the hyperspace map, temporarily layering the old storms and deep space over the new one (and creating storms where deep stacks) until the old fades away.
2) Jump gate flux: one system's jump gates all become unusable for a few months (this might explain the tutorial). Only using the navigation skill can get you out, though you can get in through gravity wells. This results in the worlds inside having serious trade issues for a while, often degrading them heavily, and trade in and out is very profitable if you can do it during that time. Trading reduces the odds of the colony entirely decivilizing... or you can make things worse, of course. A quest, perhaps requiring certain skills, might fix this, or it can clear up over time (but there are serious shortages for a while after).
3) Darkstorms: Similar to hyperspace storms but colored dramatically differently, these appear rarely but are very dangerous. They flow across the map before vanishing, but if you hit one ships can be destroyed or gain D-mods, and they accelerate you in wildly different directions, even launching you significantly around the map. Perhaps a stormfront passing through might always raise the level of hyperspace in the area... clear becomes deep, deep becomes storm, storm becomes darkstorm. Very dangerous to be caught in.
4) Hyperspace void: Similar to a Darkstorm, but stationary and draws ships toward it. Like a giant black hole in space, these fade into existence, then fade back out. While active, any ship caught in them will be ejected from hyperspace into real space... and if they're not near a star, it's going to be a VERY long trip to get anywhere else, at least until the void disperses (but even then, without the navigation skill, you can't get back to hyperspace without a jump point). If one appears over a colony, it's like an even worse version of jump gate flux, as no ships can get in or out for a long time. On the bright side they're easy to see when traveling if you're paying attention.
5) Wormholes: Appearing rarely, these last for a short time. Jumping into one shoots you out at the other end, which may be in a completely different area of the map. Some are two way, but some are one way. Using skills may let you know what it is before you go in and how long it will last. A two way wormhole can create very easy exploration for a time. Some skills may show wormholes that others can't see.
6) Hyperspace currents: These last quite a while, though might rarely shift. They create a direction of travel for the area, pushing ships in that direction. You can follow them in the right direction to save on fuel and time, though pushing against them makes for slow going indeed.
7) Ghost ships: Echoes of ships that are no longer there, these look like existing fleets, but may be missing parts (such as having too many trails for the number of ships) or may look wrong in other ways (all duplications of the same ship, flying through hyperspace at normal speed, etc). Attempting to engage them has strange effects, from having them disappear to being launched away like you just hit a hyperspace storm. Some might even allow interaction normally, yet vanish later. And sometimes you may see something impossible, like an active XIV battlegroup on approach...