The correct grammar is "had departed." This is because "departed" is the past participle form of the verb "depart," and when using the past perfect tense, we need to use the auxiliary verb "had" followed by the past participle form.
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It depends on your meaning. Sometimes people refer to a dead
person as "the departed," so you would say "the faithful departed"
in that context. However, if you mean someone left faithfully,
you'd say "they faithfully departed on their mission."