You can't. You have to go around them.
They move in regular patterns and you can jump past them in a couple of different ways, to reach the red control wheel at the upper right. When you do, the flies will leave Ratman and attack you, so Dodge them and climb the big pipe at the center to jump over to Ratman.
You do not kill the rats or the flies. The rats scurry back and forth at a regular pace on the right side, so you can dodge them and make your way up to the red control wheel. Turning the wheel will get the flies away from Ratman, but they will then attack you, forcing you to elude them and climb the large pipe at the center, from which you can jump over to Ratman. (see the related question)
When you reach the sewer room where Ratman is, he is protected by the stinging flies. Go to the right and jump between the walking rats. If you turn the final red wheel at upper right, it dumps sludge on Ratman and scares off the flies. Unfortunately, they attack you, so you will have to elude them long enough to jump up on the big pipe in the center of the room, and then over to cuff Ratman. (see related question)
Unlike the rats and flies, the roaches are just a crawly distraction in the subway before you fight with Speeding Spike. You can't affect them at all.
kill him kill him kill him kill him kill him kill him
Super mutants don't exist, so you can't kill them.
Yes he would call on 116 more power rangers overwhelming super-man
To kill a Chorizo simply shoot it with missiles or the power beam.
(The hey is wrong with you?) No, you cannot kill Luigi in Super Mario galaxy. (He's too precious)
You cannot kill the ninjas!!
jump on it
Yes
Golden eagles can kill the Catalina Island Fox.