Which villain’s backstory was the most understandable for them to become a villain in Star Trek?
I’ll nominate Annorax from Voyager’s two-part “Year of Hell.”

Annorax was a temporal scientist working for the declining Krenim Imperium. He developed a ship with a temporal weapon that, when fired, completely removed an object from the timeline, changing history so that it had never existed. Only ships with temporal shields like his would even remember the old timeline.

The Krenim fired this weapon against a rival species, erasing them from the timeline and briefly restoring the Krenim Imperium to its former glory.

Interbreeding with that species turned out to have made the Krenim immune to a deadly plague that began to run rampant throughout the empire. To correct the error, he fired again and restored almost the entire empire—except for his home colony and his beloved wife.

Annorax, never aging inside his shielded ship, spent the next two centuries rewriting the timeline to restore his wife. Each time he fired that terrible weapon, his species’ fortunes would rise and fall, but the fate of Annorax’s home and wife was never restored.

Through a large portion of the two-parter, Annorax is barely aware of Voyager; the restored Krenim Imperium is simply battering our heroes. Eventually, Voyager develops temporal shields like Annorax’s to protect themselves from Krenim torpedoes, and these shields disastrously disrupt Annorax’s subsequent firing. Annorax sets out to track down Voyager and remove it from the equation; although the ship escapes, he manages to abduct Chakotay and Paris. But he’s impressed by Chakotay, and together, they devise a way to alter history—without additional deaths—so that Voyager never encounters the Krenim in the first place.

With Chakotay’s approval, Paris provokes a mutiny that drops the temporal shields, allowing Voyager to attack and trigger a weapon overload that erases the ship from history. Commander Annorax is finally restored to his home with his wife, and he never decides to build the ship. Following the advice of a less aggressive Krenim patrol ship, Voyager slightly alters its course, unaware of the timeline it had averted.

Annorax stands out as a villain with very relatable motivations. He was not trying to exterminate all life or take over the galaxy; all he wanted to do was restore what he and his species had lost. He was the hero of his own story—always the mark of a great villain.