In MegaMan Star Force, Cygnus arrives on earth searching for a compatible human host. He discovers Tom Dubius, who had been betrayed earlier in life, and is afraid to make a BrotherBand with his boss, Aaron Boreal. Soon, a misunderstanding happens between Aaron and Tom in which Tom gets convinced that Aaron has betrayed him and taken his ideas for his own. Cygnus sees this, and so he EM Wave-Changes with Tom to become Cygnus Wing, with the plot of destroying Aaron. When Mega Man defeats him, Tom still believes that betrayal is the essence of society, and asks Aaron to prove that it isn't by taking off his helmet in a zero-oxygen, zero-gravity area. Aaron trusts Tom and therefore removes the helmet, to discover that Tom had filled the area with oxygen.
Having been proven wrong, Tom forces Cygnus away. Cygnus returns three times later in the game: first, he appears as an EX encounter in a dead end of the Lab EM road, then later as a random SP encounter, and finally he appears in the first Comp leading up to the final boss Andromeda, where you must fight him in his EX form. Each time, he assumes the form of Cygnus Wing even though he is not fused with Tom.
Cygnus appears as the "mastermind" of the FM-ian group, and the smartest of them all. He is also the first FM-ian to appear in the Anime. He first takes control over Tom Dubius at AMAKEN, after Tom thinking Aaron is about to steal his invention. He is, however, deleted when Mega Man gains his Star Break ability.