A giant empty starship, what to do?

[Fred Brackin]

I'm afraid I'm not too positive about your scenario but then let's look at some possible negatives.

I would probably avoid anything anything to do with VR. Adventures in VR are usually futile. "Victory" tends to consist of waking up and leaving VR. The exception to the futility rule is when the protagonist gets to buyoff undesired disads or raise his IQ or Will so that his real life will be improved.

I'm not sure how you'd involve time travel but time travel is usually worse than VR. Victory is usually negating whatever the time travel required and re-setting everything to the status quo ante and you don't even get to keep increased stats.

If anyone doubts these statements look what VR and time travel did to the later seasons of Agents of Shield.

There was some alternate worlds in their too and that's not as automatically futile but there's still a lot of "look how things could be worse.".

My advice might distill down to "Make sure there is a way for the PCs to achieve a real victory and reap real rewards.".

[Lovewyrm]

Dimensional split, but the ship is shared.
Don't remove all NPCs perhaps to help with that.

The gimmick is:
Both parties/sides of the coin think that the ship is acting weird, and try to fix it, which in turn surprises the other side of the dimensional coin, who then do stuff, too.
Including shutting down access points to contain what they maybe see as a computer virus or whatever (feel free to rationalize it in any way)

Perhaps the players get wise about the shared state, and the goal is to sync both parties indirectly.

Turned out that the FTL drive or some mcguffin, or a transported object caused the weird rift.

And in the end everyone is united.

"But then I will have a giant ship with NPCs and not just the players"
Yeah, it'll be great because then you can spin more stories with them.
Why cut out all that potential? Especially a ship that large and the things you could do with it...let it have some NPCs or it will feel too big and unwieldy.

P.S.: You could just have the key crew, like captains, navigators and whatever have died in the process or fallout of the process. After all, the captain gets the blame first and foremost, right?
Paranoia, mutiny, strange behaviors, etc.

So the PCs could still establish themselves as leaders of this ship in the end.

Edit:
A hostile alien third party could also come in at some point.