Note - this has significant spoilers for the Secret of the Ancients campaign.
Secret of the Ancients has some really interesting ideas and lots of detail but some serious flaws also. However, among the unbelievably coincidental timings, forced plot choices and repeatedly stripping away all of the PCs' gear, there is a serious question.
In the closing paragraphs of Chapter 4, the ship that the PCs are on:
jumps from orbit of the gas giant Komesh in Boughene (0304 in Regina subsector), to empty hex 0606 of the Regina subsector and passes through a portal to Grandfather's pocket universe.
In Chapter 5, page 91, we learn that:
[Grandfather] closed down almost all the portals leading to his pocket universe, until only one was left – the portal the Ancient ship just activated.
Then in Chapter 7 when the characters finally succeed in getting into orbit they:
enter another portal that activates, allowing them to depart the pocket universe and leaves them floating unconsciously in orbit of Boughene (?) to be captured by Arisa the Imperial spook.
What is the in-game reason for the PCs arriving there? It beats being stuck in deep space with no way to reach an inhabited system or be rescued, but otherwise it is the worst possible location because it is where their enemies are waiting for them. Note that I am not looking for game design reasons for this occurrence, which I understand, I am looking for a plausible in-game rationale.
For that matter, is it actually a typo? Assuming that the portals on each end are the same size, it would mean that a portal large enough to allow a starship to pass through is in orbit around the same planet that a scout base is located on / around without ever being detected. Was the PCs' ship actually found in the upper reaches of Komesh? Although the upper reaches of Komesh have also already been checked, and even if the PCs and IISS had failed to locate an inactive portal, it beggars belief for Seven not to have detected it when he made an appearance at the end of Chapter 4.