OKAY SO slight spoilers for various stories, here’s my headcanon about how the Infuser / Defuser gun works:

Metro Man’s powers are contained on a third strand of his DNA; that’s why Megamind was able to give Hal the powers so easily–he simply attached the third strand to the other two strands of Hal’s DNA. 

This third strand is only weakly bonded to the rest of the DNA, both in Hal and in Metro Man. The weakness of the bond is an intrinsic quality of this ‘superpowers’ DNA strand; it’s naturally only weakly bonded to the other strands. 

(This is most likely due to the fact that it was probably introduced into the DNA of the Glau artificially in the first place.)

Here’s how the Infusion process on the gun works:

Step One: A certain chemical compound, created by Megamind, is introduced into the subject’s system via dermal, mucous membrane, or soft-tissue absorption. (This means that it’ll absorb if you get it on your skin, in your mouth or up your nose like Hal, or if you’re actually shot with the gun and given a flesh wound). The golden infusion bullet Megamind creates in the film is coated in this chemical compound, and the inside of the gun is coated with it, too, so that the subject will definitely be exposed to a sufficient amount of the compound.

Step Two: This chemical compound destabilizes the subject’s DNA just slightly, which allows for

Step Three: The extra strand of DNA attaches itself to the destabilized strands of the subject’s DNA.

Step Four: The newly triple-helix DNA stabilizes.

Here’s how the Defusing process works:

Step One: The gun is fired and the chemical compound is re-introduced into the subject’s system in a spray. This is most likely going to have to be either dermal or through the mucous membrane, since the subject is now invulnerable and flesh wounds are unlikely. It’s going to absorb quicker through the mucous membrane, which is why Megamind sticking the gun in Hal’s nose was the right choice.

Step Two: The chemical compound again destabilizes the subject’s DNA allowing for

Step Three: The extra DNA strand is targeted by the gun and extracted from the subject’s system as it is drawn into the gun.

Step Four: The subject’s newly double-helix DNA stabilizes.

Megamind could temporarily take away Metro Man’s powers simply by exposing him to the destabilizing compound–since the strand with the powers is only weakly attached to the rest of the DNA, it breaks off easily, and just sort of floats around in the subject’s system. 

If Megamind didn’t extract the ‘superpowers’ DNA strand from his system during the time of DNA destabilization, Metro Man’s powers would naturally return after a while, as the ‘superpowers’ DNA strand reattached itself to the rest of the DNA. But if Megamind did extract them, they would be gone permanently.

The destabilizing compound is also useful in fuel, and in explosive devices, as it naturally destroys chemical bonds, which creates energy. When the compound is added to certain other chemicals, it causes an explosive reaction.

Which was probably how Megamind originally used the destabilizing compound; the idea of using it in the Infuser / Defuser gun came later. 

So, yes, Megamind actually did come up with a way to defeat Metro Man, but he did it while he was trying to solve a completely different problem.