In Rockman.EXE Beast, the normal Miyuki didn't appear, but a Beyondard version of her did. Her Beyondard counterpart has the same personality, except for being less mysterious than the original Miyu. Beyondard Miyu also has SkullMan and is also a secret agent. Beyondard Miyu was last seen along with Beyondard Sal and Masa witnessing peace being restored to Beyondard. This was the last appearance of Miyu in the series.
Miyuki first appears at the end episode 14 alongside Saroma, telling Masa that preparations are complete.
She appears in episode 22.
She appears in episode 24.