If you put thousands of people under ground having a few to maintain the power plant might have been thought of by somebody.

Look up 'Rickover reactor' to see just how easy it would be.
The "technology ladder" is essentially zero. All one needs is to run water through the thing. If anything the reactor can be better looked after on land than in a cylindrical boat under water. Parts cannot be manufactured on the sub like they can in a machine shop in an underground complex. If one is down just fire up another. The government can afford.
Lets say they also have knowledge of what's coming.
Lets see...this would have to be extinction event level.
Info generated by monitoring Yellowstone often gets lost.
As the solar system travels through the plane of the galaxy planetary tidal effects might be effected, or if the electric universe theory is correct it might change pretty much anything. See: Increased volcanic activity. The other planets in the solar system are also being effected. See: Global warming on Mars. Change of wind speeds on Venus. Jupiter changes its spots.
Who knows? Alien invasion? The WoW signal was from an invasion fleet approaching our solar system?

If so the good news is that they are slow.
The end of the Holocene? Although unless we went into a Snowball Earth event I doubt the return of glaciation on levels previously experienced could be considered extinction level.
Missing bio weapons? Naturally occurring pandemics? Widespread terminal hiccups?
Who knows what the government knows?