Why create a Simulation?
There are possibly two general reasons a sufficiently advanced civilization might create a simulated world/reality.
The first is Research. Developing a better understanding of the universe through the events that transpire within the simulation would be very useful. If sentient life develops, then on top of that, you can observe other life-forms, how they develop as a culture, and how they differ from the creators of this world. They could observe phenomena that in their own world is considered only theoretical, and how it might have an effect on the world or universe (depending on what scale these theories are).
The second is Entertainment. Future Hollywood has run out of ideas, so they fund a super-powerful simulation, and just record everything. They then stream the lives of more "interesting organisms", or make War movies out of the great conflicts that happened through their simulation. On the other hand, the world could be a video game, like a giant MMO that allows the origin species to log in, in place of other organisms like humans.
Why shut-down a Simulation?
So, why might the Creators decide to shut off the simulation?
In the case of a Research-Developed Simulation, there's any number of factors.
One such, being that after 13 Billion years (the simulation could probably be sped up from their perspective) they realized that the simulation is flawed. It in some fundamental way deviates in structure from the Parent Universe, and thus all of the collected research data (or at least the vast majority of it) is invalidated or discredited, rendering the continued run of the simulated world, useless.
On the other hand, "power and resources" isn't all that far-fetched a reason. For some reason people always think of "super advanced alien species" as some collective that do everything together, and because as a whole they have access to potentially unlimited energy. But this ignores the possibility that this species could have individualism. What if our current simulated reality is just a garden created by a company or organization of some kind, to research very specific ideas? Think of "Market Research" taken to an extreme. If this company suffers some sort of financial loss (assuming their species has an equivalent) continuing to maintain a live simulation may just be too costly. Or possibly a change in management could bring in someone who doesn't agree with using fancy-smancy super-simulations, and feels it's more efficient to have an AI just crunch some numbers on what would make the best T-Shirt designs.
On the other hand, the shut-down could have been the result of sabotage by another faction. Or possibly it was shut down due to protests about ethical violations. A "Just put them out of their misery," mindset could exist in this kind of society. The level of technology a species has doesn't really tell us the details of their society, so they could be just like humans, or not at all.
When it comes to simulation created for Entertainment, many of the reasons listed above are easily applicable. "They just got bored of us", is a lot like what happens to Video Games now a days anyways. What if it turned out the Sims was a real simulated reality, and by not playing, or deleting the game, you are effectively killing your sims?
Or possibly, what if the creators want to release a Universe 2, and in the process wipe out the current Universe? Or maybe Universe 3 has already been out for a while, but they haven't just yet closed the servers for Universe 1. You could say that a sufficiently advanced civilization can power a simulation of this scale all you want, but if it's just a faction within the species company, maintaining an unlimited amount of these simulations would get difficult and costly, so shutting down the older versions would just be standard. (Yes, the end of the Universe was just to make room for more sequels.)
The concept of guilt might not exist for the Origin Species. On the other hand, the Origin Species might simply not recognize us as beings worth their guilt, just like today people say that even if we created a sentient AI, they wouldn't really consider it living, or equal to another person.
In the end, there's any number of reasons, from capitalism to politics, and which ever the reason, we as a species would be unable to stop them, and unlikely to convince them otherwise.
