Examples:
Mobile Fighter G Gundam:
Spoiler (mouse over to view)
A mysterious character named Schwarz Bruder shows up and periodically helps Domon with his training. It is later discovered that Schwarz is actually Domon's brother, Kyoji, in disguise.
One Piece:
Spoiler (mouse over to view)
During the Water 7 and Enies Lobby arcs, Usopp leaves the Straw Hat Pirates, but later comes back as Sogeking.
Tales of Symphonia:
Spoiler (mouse over to view)
Although Kratos doesn't change his name or appearance, in the beginning he claims to be a simple mercenary. Later on, we discover that he has been hiding the fact that he is Lloyd's biological father, as well as one of the four Seraphim of Cruxis.
Speed Racer:
Spoiler (mouse over to view)
In certain versions of this series, it is believed that Speed's brother, Rex Racer, died in a tragic accident while racing. In reality, he is still alive, and assumed the identity of Racer X, and is trying to uncover the corruption rampant behind the scenes of racing. In some other versions, he simply left and started using his new identity.
When making the recommendations, you do not have to tell me which character it is. All I need to know is that such a character exists in the story. Please try to avoid recommending the Secret Identity tag, because there are over 500 results and it's rather vague.
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If I've made a thread in the "I'm Looking For..." forum, I am only interested in Japanese manga. I am not interested in non-Japanese media at this time.