Link later infiltrates their HQ and bests Master Kohga, their leader, sending him plummeting into a pit in a cutscene laden with foreshadowing. They show up in the background throughout BotW, attempting to assassinate Link and Zelda and leveraging an informant in Kakariko Village. The Yiga Clan first show up in Breath of the Wild, posing as common travelers on the road, only to reveal themselves in assassination attempts. There’s an excellent, untapped source of boss fights in The Legend of Zelda: Breath of the Wild and Tears of the Kingdom, but they never really quite get to shine. Which is a shame, because I like a little bit of variety in my villains.
But having the same big bad gets a little stale, and Ganondorf is truly the most prolific boss in all of the Zelda games, only occasionally yielding ground to a secondary antagonist, like Zant. While Link and Zelda are reacting to Ganon’s plots, he gets to go wild unleashing things like the Calamity and the Upheaval. Heroes save the day, but antagonists are often the ones who drive the plot forward.