Since Ganandorf now has the Triforce of Power, he's also going to pursue Wisdom and Courage (as he always does, ever since Ocarina of Time). This is the last of Ganandorf's stages but also the toughest, since Zelda and Link should be equally tough for you to beat.
Protect Zant[edit]
The first thing you should do is keep Zant out of as much danger as you can, taking down soldiers and goron officers along the way. Get him to the north where he'll unlock a door (this is where Link gets the bomb for the first time while wearing training soldier clothes in the first level). On the 3DS and Switch, if you protect Zant well enough, he'll be available for you to control.
Gorons on the run[edit]
A few important goron officers on the map are going to run to the castle located in the southwest corner. Hurry to the one closest in distance to the enemy base. If you're too late, don't ponder! Two more will come so attack them quickly. Otherwise, if will affect your officers' morale.
Impa on the run[edit]
Impa will try to run quickly to the Fairy Fountain (which you should again remember from the first level) to get help. If Ghirahim is in the south, select him and attack Impa right away, including the officers protecting her. This should be a no-brainer.
Allied Base meltdown[edit]
This will probably push you to the limit. Consider dealing with an avalanche of officers trying to take down your base - keep saboteurs, assault troops, you name it. Attack them before they reach your base or it will all be over.
Link and Zelda versus Ganondorf, Ghirahim and Zant: Showdown[edit]
Although Link comes out to attack in the beginning, he can easily be knocked down once. However, near the end, things will get tough. He'll use his power to overpower your allies, to put it simply. Zelda will come out as well. Considering the difficulty, especially on the 3DS and Switch, command everyone to protect your Allied Base to help delay the inevitable of a "Game Over". You have to attack Link and Zelda quickly before either of them recovers within a few minutes. If Link or Zelda recovers, the battle isn't over yet, so really plan ahead on this moment to finish the level.
The cutscene will show Ganondorf showing his might: he finally got all three parts of the Triforce. For the next level, it's back to the good guys, so Ganondorf's victory will be short-lived pretty soon.