I had this save file crash several times the exact same way, so if you perform
these steps exactly, you may be able to replicate the crash using either the
v0.0.5 patch by Matt Wells or the DARKFIX patch (unofficial community patch,
Test 3). It may also crash using other versions of the game, but I haven't
tested this myself.

First of all, there are two missions currently active. The main plot is
complete, but the only complete cinematic mission is Louissa Phillips (part 1);
as usual, part 2 failed to happen. I received the email from Xavier Shondi to
meet him at the Surgeons Blunder Bar on Crius for his first cinematic mission,
and I've been to see him there and accepted the mission. I also accepted a BBS
mission: "University of Hermes, College of Biological Research" which involves
flying between Destinas and Draknor, destroying a few Kindred ships for 3,700
Credits.

So I could be wrong, but I think the crash has to do with the system of storing
ships to the number keys (it says 1-9 in the Help menu and manuals / quick
reference cards, but 0 works as well.) There is a known glitch that happens
under certain circumstances: if you store a ship that is part of a mission and
the ship lands, jumps out of the game completely or otherwise disappears
(destroying it might count as well), then new ship(s) jump into the area, one
of the new ships may overwrite the stored ship in memory, meaning pressing the
hotkey will now select that new ship. I don't know whether any of this is part
of the cause of the glitch, but it might be, because it didn't crash for me one
time when I didn't use the hotkeys to save the ship in question. However, since
Xavier's Arms Shipment has another escort ship, when the shipment lands, the
escort will stop moving but if another ship fills the slot in memory where the
shipment was, the escort will now defend THAT ship instead, even if it's a
pirate ship! Again, this may not be relevant in the case of this crash because
I jumped away straight away after the shipment landed, but for completeness I
mention this.

Here's what I did. I left Crius, stored the Arms Shipment as hotkey 1 and
stored the Heretic (its other escort) as hotkey 2. I also flew close enough to
the Heretic to scan it, although that again may not be necessary. Having set my
destination to Nav Point #0, Karatikus, I escorted the Arms Shipment there and
watched it until it landed. (It's possible to instantly complete the mission by
jumping away when it's in Karatikus's space and approaching the planet, even if
it's still quite far from the planet when you jump, but I didn't do this.)

After completing this mission, I went to System Jump 5A (#204), jumped through
to System Jump 5B (#102) and continued to Destinas and Draknor, completing the
other mission. After Draknor, I set Crius as my destination, intending to land
there to finish Xavier's mission, but the game crashed about two jumps after
leaving the area of Draknor.

I finally managed to avoid a crash by not storing any ships to hotkeys and
sending the Arms Shipment on its way while doing the other mission. This took
a few tries as it's pot luck whether the cargo will make it there or not, but
by doing it this way, it didn't crash.

Since it happened the same way multiple times, I think it could be to do with
bad data left over in memory for mission-generated ships. Maybe something
overflowed its memory location, or maybe the game tried to clear the wrong
memory after a mission ended? No idea.

Matt