This is by far one of the weirdest final encounters you'll experience in a video game, let alone a Metroid title. You'll be rooted to the spot, stuck in first-person view as Samus protects Madeline from the swarm of Desbrachians around the room. MB's not kidding around, these pesky bugs are not friendly.
Despite trading blows with the Galactic Federation marines, some of the Desbrachians will fill your view and take swipes at Samus. There's no chance to Sensemove or use Concentration, and firing Missile after Missile into the bugs will only knock them around and eventually send them into a regenerative state before they resume attacking.
This odd encounter requires an equally-odd method to end it. It's once again a rewarding moment if you can figure it out for yourself, so here's a few hints to start with:
Keep your eyes on the battle as you knock Desbrachians around and look very carefully for something interesting in the room. It's not the Desbrachians nor the Federation Marines. Nothing on the walls either. Once you see it, you should instinctively know exactly what do to - target it and open fire!
If that doesn't help, click below for the answer:
Take note that this battle needs to be finished exceptionally fast on Hard mode, before the Desbrachians can drain your single Energy Tank. As soon as the battle begins, try to lock on and hit the first Desbrachian with a Missile before it attacks Samus. That should knock it out of the way and give you a chance to take action to end the battle immediately. Finish the scenario and enjoy the finale!