The past perfect tense of the sentence "By the time the storm hit they had already evacuated the entire town" is "had already evacuated".
The past perfect tense of the sentence "By the time the storm hit they had already evacuated the entire town" is "had already evacuated".
The past perfect tense is used to describe an action that was completed before another action in the past. In this sentence, the action of evacuating the entire town was completed before the storm hit.
Example: By the time I arrived at the party, they had already eaten all the food.