The home planet of a race is completely annihilated (hit by another planet or something), but they managed to launch a generation ship beforehand, and a few thousand people go on a century-long trip to another habitable planet.
Now, there is a bad guy, some kind of time lord. He has the power to reset a certain area of space - and everything in it - to a former instance.
Now, for whatever reason, the bad guy chooses to repeatedly reset the ship and crew to a former time (a day? a month?), which basically means the ship is set back millions of km and will never reaches its destination. The crew does not notice the time loop, as their brains are reset with the rest of the ship. (lets ignore the fact that there may still be ways for them to find out otherwise.)
So, here is the question. What motives are there for the bad guy that he could not achieve by simply destroying the generation ship?
Excited to hear your ideas :)