When will the time come?"
This is the standard question form of when + "the time will come." You want to know when.
When the time will come?
You can "questionify" a statement, or phrase that could validly extend a statement by adding a question mark at the end, without changing the word order.
This turns the statement into a request for acknowledgement. The appropriate answers here are only yes or no, or something that evaluates to no, but X instead.
This is what it sounds like your doing with this example. You already know when, you simply want acknowledgement.
Other examples to illustrate:
A: I'm going to the park.
B: Where Sally is? (B knows Sally went to the park earlier and believes that's why A is going there. This is valid because you could say I'm going to the park where Sally is.)
A: Yes. (Acknowledged)
A: I'm going to try to find my dog.
B: The brown dog? (Again, it's valid if A said I'm going to try to find my dog, the brown dog)
A: I'm looking for the black one. (= "No, I'm looking for the black one instead.")