Being the continuation of Rockman.EXE Axess and the third anime in the Rockman.EXE anime series, Rockman.EXE Stream takes place right where Axess left off, with Netto and Rockman's battle against Dr. Regal, leader of Nebula. Now, something greater poses a threat for the Earth, and it's name is Duo. A mysterious net navi from space, his mission is to erase planets that are living with darkness. Because of the constant evil lurking from Regal's Dark Chips, Duo is set out to destroy Earth. But can Netto and Rockman prove to him that Earth is full of good?

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Prequel: Rockman.EXE Axess
Side story: Gekijouban Rockman.EXE: Hikari to Yami no Program
Sequel: Rockman.EXE Beast
Alternative setting: Irregular Hunter X