He first appeared in "Donald Duck" #102 as a rival inventor for Gyro Gearloose.
Later on, he was adopted into the Mickey Mouse universe as an enemy for Mickey Mouse and his friends, in particular Super Goof.
Emil has caused a lot of trouble for Mickey Mouse, Super Goof, Donald Duck, Scrooge McDuck, Gyro Gearloose, and other characters on various occaisions. Sometimes he has teamed up with Black Pete, the Beagle Boys, Mad Madam Mim or other bad guys in the Mickey Mouse universe or the Donald Duck universe. It's hard to tell which universe he really belongs in.
Emil Eagle makes Cameo Appearance in the Episode of the Darkwing Duck : In Like Blunt.