Learn Spanish (Spain): ¿Qué hora es?

In Spanish, tiempo refers to the weather or time in a general sense, like having free time. When you want to ask for the time on a clock, you always use hora, which literally means hour. You are essentially asking what hour it is.

If I know the answer will be plural like Son las tres, why does the question use the singular es?

The question is always asked in the singular because you are asking about the current hour, which is the singular word hora. Even though the answer switches to the plural son for hours two through twelve, the question remains fixed as ¿Qué hora es?.

Can I ever ask ¿Qué horas son? if I think it is late?

In Spain, the standard and most natural way to ask for the current time is strictly the singular ¿Qué hora es?. You do not make it plural, no matter how late in the day you think it might be!

How does this change if I want to ask what time a train leaves or a movie starts?

This specific sentence, ¿Qué hora es?, is only used to ask for the current time on the clock right now. If you want to ask at what time a scheduled event happens, you have to add the word A to the beginning, making it ¿A qué hora...?.