The Wily Army is the combined might of Dr. Wily's Robot Master squadrons and the many mechaniloids and drones that make up the entirety of it. They oppose the Repliforce and Maverick Hunters primarily, though have been known to see anyone else as a potential threat or target.
In short, the subjugation of the UN led governments (protected by Repliforce and world domination.
The average individual in the Wily Army is either one of his personally built Robot Masters, or the odd mech or drone. Most of the Robot Masters in the WA are built by Dr. Wily himself, although he has been known to 'appropriate' a few for positions in his army from the public or various agencies.