Earlier this month, a brand new Rockman EXE comic debuted in Coro Coro Special, sister magazine of Coro Coro Comics. Info was a bit on the scarce side, but fortunately, we now have ourselves a fairly detailed summary courtesy of Tarbosan.
Rockman EXE Vs. Operate Shooting Star, depicts a heated battle between Rockman.EXE and Shooting Star Rockman. RockEXE's operator, Raito Amino, is determined to become a strong Net Battler after having lost a battle with his friend.
On his quest to become stronger, Raito comes across an elder Net Battler who criticizes Raito's fighting style, noting his lack of strategy as his one true weakness. Challenging him to a duel, Raito finds himself pitted against Shooting Star Rockman. The bout comes to an end when SSR is defeated. The end.
It's a simple story, one that may or may not continue in the following issue due to it being touted as a "one-shot." Still, there's definitely room for more stories.
A few more scans of the issue available at Tarbosan's blog.