EM Viruses are viruses that plague the Wave Road and the Earth since it is covered with EM Waves. They cause disturbances in the Wave Road which causes machines and anything running on EM Waves to break down.
Viruses are enemies commonly found through random encounters whilst on the Wave Roads. These viruses often appear in groups of 2 to 3, and sport low HP, but an inability to flinch or enter Invisibility like bosses. Deleting virus groups will net the player a reward, usually Zenny or a Battle Card given from one of the viruses, depending on the Busting rank.
The player can also encounter G(G for "Giga" as these viruses are much bigger) versions of these viruses, which sport double HP and double damage (in Shooting Star Rockman 3 the multiplier is x1.5 instead). These viruses are encountered in MegaMan Star Force in plot-relevant encounters and do not yield any reward upon defeat; in MegaMan Star Force 2 they will yield Star Cards that power up Battle Cards of the same name; in Shooting Star Rockman 3 they appear in Warning Battles, give only Zenny, and allow for MegaMan to stand a chance at gaining a Noise Change.
Viruses can also be located and battled in the real world whilst as MegaMan, in Shooting Star Rockman 3. Heading up to them and pressing A will launch MegaMan into a fight, with a reward at the end as usual depending on the Busting rank. Defeating all viruses in the real world is a requirement to opening one of the doors in the secret area of said game.
In the first game, at the very start of the game, a man will tell Geo that the Satellite Admins are responsible for deleting viruses before the land on Earth, implying EM Viruses' origins are from Outer Space, and there were none on Earth originally. Also, Battle Cards were created 3 years prior to the first game in order to delete the EM Viruses who has been showing up.
In the 2nd game, however, there are new viruses that show up due to Mu's rise, which means there were EM Viruses on Earth, although they were in "suspended animation" prior to Mu's 2nd rise.