Mike Gamble, a producer on the Mass Effect series, reveals that the BioWare team in charge of the series initially created an ending for the third game which involved a boss fight that pitted protagonist Commander Shepard against a version of the Illusive Man, which was enhanced by reaper technology.
The developer tells Gamer Syndrome that, “We also scrapped the original ending for Mass Effect 3. We were gonna have it as a 'boss battle', where Commander Shepard would go up and fight The Illusive Man who has been transformed by the Reapers. We scrapped that idea because way too many have that as their ending, some final boss fight.”
BioWare has ended up with a game conclusion that transforms the entire galaxy and which some players have found questionable.
Since then, the Final Cut DLC has modified some of the details.