Look at the following phrases (bold) in the original sentence:
"In the early morning, the sky had darkened and then it will rain."
These do not agree with one another. "Had darkened" is past perfect tense while "will rain" is future tense. Therefore, we can eliminate NO CHANGE as a valid answer.
The second option contains both "will darken" (future tense) and "rained" (past tense). These do not agree with one another. Therefore, this answer can be eliminated.
The fourth option contains both "is darkening" (present tense) and "had rained" (past perfect tense). These do not agree with one another. Therefore, this answer can be eliminated as well.
The third option contains "darkened" (past tense) and "rained" (past tense). These agree with one another. Therefore, the correct answer is:
"...darkened and then it rained."
I hope this helps!
